Error running CWL. WorkflowOutputParameter are not supported

Hi,
I am trying to run a CWL workflow with a single input and output files, which is essentially writing the contents of one text file (input) to another (output)

The tool is the following:
cat.cwl:

class: CommandLineTool
cwlVersion: v1.0
id: cat_test
baseCommand:
  - cat
inputs:
  - id: input
    type: File
    inputBinding:
      position: 0
outputs:
  - id: output
    type: File
    outputBinding:
      glob: '*.out'
label: cat-test
requirements:
  - class: DockerRequirement
    dockerPull: 'ubuntu:latest'
  - class: InlineJavascriptRequirement
stdout: '${ return inputs.input.basename + ".out" }'

The workflow wf_cat.cwl is the following:

class: Workflow
cwlVersion: v1.0
id: wf_cat
label: wf_cat
inputs:
  - id: input
    type: File
outputs:
  - id: output
    outputSource:
      - cat_test/output
    type: File
steps:
  - id: cat_test
    in:
      - id: input
        source: input
    out:
      - id: output
    run: cat-test.cwl
    label: cat-test
requirements: []

The input file used to run the workflow cat.yml is the following:

input: /Users/cromwell/test/testInput.txt

This workflow exits with the error:

$java -jar cromwell-36.jar run wf_cat.cwl -i cat.yml -p cat.zip --type cwl

[error] WorkflowManagerActor Workflow a07915f9-fdfd-46c0-867d-3db266c9760e failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
Workflow output parameters such as WorkflowOutputParameter(file:///var/folders/34/kzv1pzl57s92dbz54rvr1px00000gn/T/cwl_temp_dir_6240076588655691693/cwl_temp_file_a07915f9-fdfd-46c0-867d-3db266c9760e.cwl#output,None,None,None,None,None,None,Some(Inr(Inl([Ljava.lang.String;@3775df9c))),None,Some(Inl(Inl(File)))) are not supported.
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:214)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:184)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:179)
    at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
    at akka.actor.FSM.processEvent(FSM.scala:684)
    at akka.actor.FSM.processEvent$(FSM.scala:681)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:135)
    at akka.actor.LoggingFSM.processEvent(FSM.scala:820)
    at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:135)
    at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678)
    at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672)
    at akka.actor.Actor.aroundReceive(Actor.scala:517)
    at akka.actor.Actor.aroundReceive$(Actor.scala:515)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:135)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
    at akka.actor.ActorCell.invoke(ActorCell.scala:557)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
    at akka.dispatch.Mailbox.run(Mailbox.scala:225)
    at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
    at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
    at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
    at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
    at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

[2019-01-08 21:56:50,01] [info] WorkflowManagerActor WorkflowActor-a07915f9-fdfd-46c0-867d-3db266c9760e is in a terminal state: WorkflowFailedState

Any advice?

Thanks in advance for your help

Answers

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