Update: July 26, 2019
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.

ERROR: No more tokens. Expecting rparen

I'm having a problem getting Cromwell (36) to parse my WDL file using PAPI V2 where I encounter this error:

2019-01-04 02:55:37,567 cromwell-system-akka.dispatchers.engine-dispatcher-26 ERROR - WorkflowManagerActor Workflow a26aec5b-a782-469a-917a-81563f766559 failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
ERROR: No more tokens. Expecting rparen

Array[Int] scatter_index = range(stage

Anyone know why this would be happening if the same WDL file was parsed without a problem under PAPI V1?

One of the main differences between V1 and V2 is that with V1 you were able to pass along the entire contents of the WDL file in the RunPipelineArgs Java class but this doesn't exist in V2 so I had to create a workaround to get the WDL runner Python script the WDL file (by retrieving a base64 encoded version of the WDL file and then decoding it).

A more complete stack trace is here in this gist: gist.github.com/edpark/9a0fb4401cec3b2d37da711b010e619e


  • For what it's worth, the WDL file passes validation using the validator found in wdltool.jar
  • ChrisLChrisL Cambridge, MAMember, Broadie, Moderator, Dev admin

    Hi @edpark_clearlabs,

    The WDL parsing step happens in Cromwell before it considers backends so from the Cromwell side, that feels like a red herring to me. I suspect this is more to do with the difference between how you (or wdl_runner) are packaging the WDL for submission to Cromwell.

    Could you give us some more details on how you used to run the workflow, and how you're running it now? (eg are you using Java or python? Or wdl_runner? And if so, which wdl_runner versions you were using, the command line, etc)?


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