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Differences between running wdl scripts with wdl-runner versus java -jar cromwell.jar

mack812mack812 SpainMember


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 run command (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

Post edited by mack812 on


  • mack812mack812 SpainMember
    edited May 21

    Hi there,

    It has been some time now so it seems that my question was left unanswered. Sorry to insist on this but I really need to now what are the differences in running Cromwell from a terminal in my local machine (with java and a .conf file) versus doing it from the wdl-runner folder using the gcloud alpha genomics pipelines run command (this is the option that I am currently using).

    I would really appreciate if I could get an answer this time.

    Thank you in advance

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