We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Differences between running wdl scripts with wdl-runner versus java -jar cromwell.jar
I am still quite new to wdl scripts and running wdl scripts in GCP via Cromwell. During my short experience with wdl+Cromwell, I have been using the wdl-runner hosted here all along, following the instructions detailed here. I chose to do so because I understood that this is a simpler way than running wdl scripts with a config file as explained here
But now I am realizing that some of the newer capabilities of the wdl language such as computing the size of an array of files with
size(Array[File], "GB") make the process crash when running wdl scripts with the wdl-runner. Here is a snippet of an error of this kind:
2019-03-11 12:12:42,294 cromwell-system-akka.dispatchers.engine-dispatcher-25 ERROR - WorkflowManagerActor Workflow eaffc40f-be93-428b-8550-b52b7b1942a9 failed (during ExecutingWorkflowState): cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for MergeVCFs: Failed to evaluate input 'disk_size' (reason 1 of 1): The 'size' method expects a 'File' or 'File?' argument but instead got Array[File]. at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1.applyOrElse(JobPreparationActor.scala:66) at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1.applyOrElse(JobPreparationActor.scala:62)
Hence, my questions are:
- Is the version of Cromwell used by GCP when wdl scripts are run with the
gcloud alpha genomics pipelines runcommand (i.e. with the wdl-runner) the same as the latest release hosted here?. If not, what is the version used?
- Will the latest developments of the wdl language be only available when running Cromwell in command line (i.e. via
java -Dconfig.file=google.conf -jar cromwell-29.jar run hello.wdl -i hello.inputs)?
- Is it a better idea not to use the wdl-runner, and use the command line version instead, in order to harness the full power of the wdl language?
Thank you in advance