Add support for namespaced inputs again.

CHANGELOG.md

@@ -7,7 +7,14 @@
 + Fix a bug where zip files with directories could not be imported. 
   For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl` 
   and `imports/b.wdl` could not.
-
+
+### WDL
++ Namespaces in inputs JSON files are handled differently. This only affects inputs for
+  tasks (or subworkflows) in subworkflows. For example `my_workflow.sub_wf_file.sub_wf_name.my_task.my_input`
+  will change to `my_workflow.sub_wf_name.my_task.my_input`. More information can be 
+  found in [the documentation on inputs](https://cromwell.readthedocs.io/en/stable/Inputs).
+
+
 ## 48 Release Notes
 
 ### Womtool Graph for WDL 1.0

docs/Inputs.md

@@ -0,0 +1,131 @@
+## Inputs
+
+Inputs are specified as a JSON file. The JSON file can be passed to cromwell by using the
+`-i` of `--inputs` command line flag. See the [command line documentation](CommandLine.md) 
+for more information. Check the [API documentation](api/RESTAPI.md) for information on how
+to pass inputs to a cromwell server.
+
+### Example
+
+Given the following workflow
+
+***hello.wdl***
+```WDL
+version 1.0
+task hello {
+  input {
+    String addressee
+    String? optionalText
+  }  
+  command {
+    echo "Hello ~{addressee}! Welcome to Cromwell . . . on Google Cloud!"
+    ~{"echo " + optionalText}
+  }
+  output {
+    String message = read_string(stdout())
+  }
+  runtime {
+    docker: "ubuntu:latest"
+  }
+}
+
+workflow wf_hello {
+  input {
+      String addressee
+  }
+  call hello {
+    input:
+      addressee=addressee
+  }
+
+  output {
+     String message = hello.message
+  }
+}
+```
+
+The following inputs file contains all the required inputs.
+***hello.inputs***
+```JSON
+{
+  "wf_hello.addressee": "World"
+}
+```
+
+The inputs file can also be used to specify task level inputs.
+
+```json
+{
+  "wf_hello.addressee": "World",
+  "wf_hello.hello.optionalText": "This is submitted into the task input directly."
+}
+```
+
+### Advanced: namespacing in inputs files.
+
+Cromwell uses namespacing to make sure all inputs are addressable in a comprehendable manner.
+In the above example the `wf_hello` workflow has its own namespace. In this namespace reside:
++ `addressee`, an input string
++ `hello`, a task
++ `message`, an output string
+
+In the inputs file all inputs are addressable by namespace. So `addressee` is accessible as
+`wf_hello.addressee`. This also allows access to all inputs of the task `hello` such as
+`wf_hello.hello.optionalText`.
+
+If a more complicated workflow with lots of subworkflows is used the namespaces can be used as
+well.
+
+```wdl
+version 1.0 
+
+import "subworkflow1.wdl" as wf_one
+import "subworkflow2.wdl" as wf_two
+
+workflow MainWorkflow {
+  input {
+    File dataFile
+    String method      
+  }    
+  call wf_one.Workflow as WorkflowOne {
+    input:
+       data = dataFile
+  }                    
+  call wf_two.Workflow as WorkflowTwo {
+     input:            
+       data = WorkflowOne.analysedData,
+       method = method
+  }        
+  output {
+     File processedData = WorkflowTwo.methodicallyAnalyzedData
+     File report = WorkflowTwo.report            
+  }
+}
+```
+
+The following inputs are required
+```json
+{
+  "MainWorkflow.dataFile": "/path/to/data",
+  "MainWorkflow.method": "thorough"      
+}
+```
+
+Using namespaces, subworkflow tasks can also be addressed.
+```json
+{
+  "MainWorkflow.dataFile": "/path/to/data",
+  "MainWorkflow.method": "thorough",
+  "MainWorkflow.WorkflowOne.nested_task.obscureParameter": 42,
+  "MainWorkflow.WorkflowTwo.summarize.reportType": "html"
+}
+```
+
+This feature allows users to specify inputs for deeply nested subworkflows as well:
+```json
+{
+  "MainWorkflow.dataFile": "/path/to/data",
+  "MainWorkflow.method": "thorough",
+  "MainWorkflow.WorkflowOne.AnotherSubworkflow.DeeplyNestedWorkflow.analysisTask.kmerSize": 22
+}
+```

wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala

@@ -53,8 +53,7 @@ object CallElementToGraphNode {
       }
 
     def supplyableInput(definition: Callable.InputDefinition): Boolean = {
-        !definition.isInstanceOf[FixedInputDefinitionWithDefault] &&
-        !definition.name.contains(".") // NB: Remove this check when sub-workflows allow pass-through task inputs
+        !definition.isInstanceOf[FixedInputDefinitionWithDefault]
     }
 
     def validInput(name: String, definition: Callable.InputDefinition): Boolean = {

womtool/src/test/resources/inputs/wdl_draft3/cnv_somatic_pair_workflow/all.inputs.json

@@ -32,21 +32,25 @@
   "CNVSomaticPairWorkflow.CollectCountsTumor.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.kernel_approximation_dimension": "Int? (optional)",
   "CNVSomaticPairWorkflow.outlier_neutral_segment_copy_ratio_z_score_threshold": "Float? (optional)",
+  "CNVSomaticPairWorkflow.CNVOncotatorWorkflow.OncotateSegments.basename_called_file": "String? (optional)",
   "CNVSomaticPairWorkflow.kernel_variance_copy_ratio": "Float? (optional)",
   "CNVSomaticPairWorkflow.CallCopyRatioSegmentsTumor.use_ssd": "Boolean (optional, default = false)",
   "CNVSomaticPairWorkflow.additional_args_for_oncotator": "String? (optional)",
   "CNVSomaticPairWorkflow.format": "String? (optional)",
+  "CNVSomaticPairWorkflow.CNVOncotatorWorkflow.OncotateSegments.use_ssd": "Boolean (optional, default = false)",
   "CNVSomaticPairWorkflow.DenoiseReadCountsTumor.use_ssd": "Boolean (optional, default = false)",
   "CNVSomaticPairWorkflow.mem_gb_for_model_segments": "Int? (optional)",
   "CNVSomaticPairWorkflow.mem_gb_for_plotting": "Int? (optional)",
   "CNVSomaticPairWorkflow.min_total_allele_count": "Int? (optional)",
   "CNVSomaticPairWorkflow.ref_fasta": "File",
   "CNVSomaticPairWorkflow.ModelSegmentsNormal.use_ssd": "Boolean (optional, default = false)",
+  "CNVSomaticPairWorkflow.CNVOncotatorWorkflow.OncotateSegments.machine_mem_mb": "Int? (optional)",
   "CNVSomaticPairWorkflow.num_burn_in_allele_fraction": "Int? (optional)",
   "CNVSomaticPairWorkflow.smoothing_threshold_allele_fraction": "Float? (optional)",
   "CNVSomaticPairWorkflow.ModelSegmentsTumor.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.mem_gb_for_collect_counts": "Int? (optional)",
   "CNVSomaticPairWorkflow.ref_fasta_dict": "File",
+  "CNVSomaticPairWorkflow.CNVOncotatorWorkflow.OncotateSegments.disk_space_gb": "Int? (optional)",
   "CNVSomaticPairWorkflow.minimum_contig_length": "Int? (optional)",
   "CNVSomaticPairWorkflow.smoothing_threshold_copy_ratio": "Float? (optional)",
   "CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosNormal.output_dir": "String? (optional)",
@@ -72,6 +76,7 @@
   "CNVSomaticPairWorkflow.PreprocessIntervals.use_ssd": "Boolean (optional, default = false)",
   "CNVSomaticPairWorkflow.mem_gb_for_collect_allelic_counts": "Int? (optional)",
   "CNVSomaticPairWorkflow.normal_bam": "File? (optional)",
+  "CNVSomaticPairWorkflow.CNVOncotatorWorkflow.OncotateSegments.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.CollectCountsNormal.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.CollectAllelicCountsTumor.use_ssd": "Boolean (optional, default = false)",
   "CNVSomaticPairWorkflow.num_burn_in_copy_ratio": "Int? (optional)",