use readme Rmd

.Rbuildignore

@@ -9,3 +9,4 @@ docker
 ^pkgdown$
 ^.lintr$
 man-roxygen/
+^README\.Rmd$

README.Rmd

@@ -0,0 +1,144 @@
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r include=FALSE}
+knitr::opts_chunk$set(
+  comment = "#>",
+  collapse = TRUE,
+  warning = FALSE,
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# rcromwell
+
+<!-- badges: start -->
+[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.github.io/badges/badges/experimental.svg)](https://getwilds.github.io/badges/#experimental)
+[![R-CMD-check](https://github.com/getwilds/rcromwell/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/getwilds/rcromwell/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+Convenience Tools for Managing WDL Workflows via Cromwell
+
+## Installation
+
+You can install the development version of `rcromwell` from [GitHub](https://github.com/) with:
+
+```r
+# install.packages("remotes")
+remotes::install_github("getwilds/rcromwell")
+```
+
+Install a specific release version (in this case v1.0) by:
+
+```r
+remotes::install_github('getwilds/rcromwell@v1.0')
+```
+
+## Set up your Cromwell Server
+
+Use instructions over in the [diy-cromwell-server repo](https://github.com/FredHutch/diy-cromwell-server) to get the configuration files needed and some testing workflows.
+
+
+## Example workflow process
+
+Set your Cromwell URL
+
+```r
+cromwell_config("http://gizmoXXX:20202")
+```
+
+### Validate your workflow formatting
+
+```r
+list.files(pattern = "*.wdl")
+valid <- cromwell_validate(WDL = "myworkflow.wdl")
+valid[["errors"]]
+```
+
+### Go fix your issues, now send your workflow to Crowmell
+
+```r
+thisJob <- cromwell_submit_batch(WDL = "myworkflow.wdl",
+                    Params = "myworkflow-parameters.json",
+                    Batch = "myworkflow-batch.json",
+                    Options = "workflow-options.json")
+(thisOne <- thisJob$id)
+```
+
+`thisJob$id` is the unique Cromwell ID for your entire workflow - you can use that to request all sorts of metadata!!!
+
+### Now get all your metadata and track the workflow!!
+
+Return a data frame of all jobs run in the past number of days (uses your database)
+
+```r
+jobs <- cromwell_jobs(days = 2)
+```
+
+Return a data frame (one line if you only submit one workflow id) containing workflow level metadata
+
+```r
+w <- cromwell_workflow(thisOne)
+```
+
+Print the current status of the workflow(s) is(are)
+
+```r
+w$status
+```
+
+Return a data frame containing all call level metadata
+
+```r
+c <- cromwell_call(thisOne)
+```
+
+Handy set of dplyr commands to tell you about how the various calls are doing
+
+```r
+c %>% group_by(callName, executionStatus) %>% summarize(status = n()) %>% arrange(executionStatus)
+```
+
+Returns a data frame containing call level call caching  metadata
+
+```r
+ca <- cromwell_cache(thisOne)
+```
+
+Handy set of dplyr commands to tell you about what sort of call caching is happening
+
+```r
+ca %>% group_by(callCaching.hit, callName) %>% summarize(hits = n())
+```
+
+Opens up a popup in your browser with a timing diagram in it.
+
+```r
+cromwell_timing(thisOne)
+```
+
+Returns a data frame containing call level failure metadata
+
+```r
+f <- cromwell_failures(thisOne)
+```
+
+Will tell Cromwell to abort the current workflow - note this cannot be undone and it will take a while to stop all the jobs.
+
+```r
+abort <- cromwell_abort(thisOne)
+```
+
+When a workflow is done, request information about the workflow outputs.
+
+```r
+out <- cromwell_outputs(thisOne)
+```
+
+### Misc stuff
+
+Ugly list of raw metadata should you need it for workflow troubleshooting
+
+```r
+cromwell_glob(thisOne); WTF[["failures"]]
+```

README.md

@@ -1,93 +1,136 @@
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+
+
 # rcromwell
 
-R package for using Cromwell with WDL workflows.
+<!-- badges: start -->
+[![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.github.io/badges/badges/experimental.svg)](https://getwilds.github.io/badges/#experimental)
+[![R-CMD-check](https://github.com/getwilds/rcromwell/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/getwilds/rcromwell/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
 
+Convenience Tools for Managing WDL Workflows via Cromwell
 
-## Install from GitHub
+## Installation
 
-Install the most recent version of `rcromwell`:
+You can install the development version of `rcromwell` from [GitHub](https://github.com/) with:
 
 ```r
-require(remotes)
-remotes::install_github('getwilds/rcromwell')
+# install.packages("remotes")
+remotes::install_github("getwilds/rcromwell")
 ```
 
 Install a specific release version (in this case v1.0) by:
+
 ```r
-require(remotes)
 remotes::install_github('getwilds/rcromwell@v1.0')
 ```
 
 ## Set up your Cromwell Server
 
-Use instructions over in the [diy-cromwell-server repo](https://github.com/FredHutch/diy-cromwell-server) to get the configuration files needed and some testing workflows.  
+Use instructions over in the [diy-cromwell-server repo](https://github.com/FredHutch/diy-cromwell-server) to get the configuration files needed and some testing workflows.
 
 
 ## Example workflow process
 
-```{r}
-## Set your Cromwell URL
-setCromwellURL(nodeAndPort = "gizmoXXX:20202")
+Set your Cromwell URL
+
+```r
+cromwell_config("http://gizmoXXX:20202")
 ```
 
 ### Validate your workflow formatting
 
-```{r}
+```r
 list.files(pattern = "*.wdl")
-valid <- cromwellValidate(WDL = "myworkflow.wdl"); valid[["errors"]]
+valid <- cromwell_validate(WDL = "myworkflow.wdl")
+valid[["errors"]]
 ```
-## Go fix your issues, now send your workflow to Crowmell
 
-```{r}
-thisJob <- cromwellSubmitBatch(WDL = "myworkflow.wdl",
+### Go fix your issues, now send your workflow to Crowmell
+
+```r
+thisJob <- cromwell_submit_batch(WDL = "myworkflow.wdl",
                     Params = "myworkflow-parameters.json",
                     Batch = "myworkflow-batch.json",
                     Options = "workflow-options.json")
+(thisOne <- thisJob$id)
+```
+
+`thisJob$id` is the unique Cromwell ID for your entire workflow - you can use that to request all sorts of metadata!!!
 
-# thisJob$id is now the unique Cromwell ID for your entire workflow - you can use that to request all sorts of metadata!!!
-thisOne<- thisJob$id; thisOne
+### Now get all your metadata and track the workflow!!
+
+Return a data frame of all jobs run in the past number of days (uses your database)
+
+```r
+jobs <- cromwell_jobs(days = 2)
 ```
 
-## Now get all your metadata and track the workflow!!
+Return a data frame (one line if you only submit one workflow id) containing workflow level metadata
 
-```{r}
-# Returns a data frame of all jobs run in the past number of days (uses your database)
-jobs <- cromwellJobs(days = 2)
+```r
+w <- cromwell_workflow(thisOne)
+```
 
-# Returns a data frame (one line if you only submit one workflow id) containing workflow level metadata
-w <- cromwellWorkflow(thisOne)
+Print the current status of the workflow(s) is(are)
 
-# This is handy to print the current status of the workflow(s) is(are)
+```r
 w$status
+```
+
+Return a data frame containing all call level metadata
+
+```r
+c <- cromwell_call(thisOne)
+```
 
-# Returns a data frame containing all call level metadata
-c <- cromwellCall(thisOne)
+Handy set of dplyr commands to tell you about how the various calls are doing
 
-# Handy set of dplyr commands to tell you about how the various calls are doing
+```r
 c %>% group_by(callName, executionStatus) %>% summarize(status = n()) %>% arrange(executionStatus)
+```
+
+Returns a data frame containing call level call caching  metadata
+
+```r
+ca <- cromwell_cache(thisOne)
+```
 
-# Returns a data frame containing call level call caching  metadata
-ca <- cromwellCache(thisOne)
+Handy set of dplyr commands to tell you about what sort of call caching is happening
 
-# Handy set of dplyr commands to tell you about what sort of call caching is happening
+```r
 ca %>% group_by(callCaching.hit, callName) %>% summarize(hits = n())
+```
 
-# Opens up a popup in your browser with a timing diagram in it.
-cromwellTiming(thisOne)
+Opens up a popup in your browser with a timing diagram in it.
 
-# Returns a data frame containing call level failure metadata
-f <- cromwellFailures(thisOne)
+```r
+cromwell_timing(thisOne)
+```
 
-# Will tell Cromwell to abort the current workflow - note this cannot be undone and it will take a while to stop all the jobs.  
-abort <- cromwellAbort(thisOne)
+Returns a data frame containing call level failure metadata
 
-# When a workflow is done, request information about the workflow outputs.
-out <- cromwellOutputs(thisOne)
+```r
+f <- cromwell_failures(thisOne)
 ```
 
-## Misc stuff
+Will tell Cromwell to abort the current workflow - note this cannot be undone and it will take a while to stop all the jobs.
 
-```{r}
-# Ugly list of raw metadata should you need it for workflow troubleshooting
-WTF <- cromwellGlob(thisOne); WTF[["failures"]]
+```r
+abort <- cromwell_abort(thisOne)
+```
+
+When a workflow is done, request information about the workflow outputs.
+
+```r
+out <- cromwell_outputs(thisOne)
+```
+
+### Misc stuff
+
+Ugly list of raw metadata should you need it for workflow troubleshooting
+
+```r
+cromwell_glob(thisOne); WTF[["failures"]]
 ```