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"Exception in thread "main" scala.MatchError: null" Validating my WDL

bshifawbshifaw Member, Broadie, Moderator admin
edited September 2018 in Ask the Cromwell + WDL Team

I'm working on the five-dollar-genome-analysis-pipeline which uses several subworkflows and sub-subworkflows. I've edited the script to have additional tasks and variables, but when testing the script the errors below are received. How can I make sense of the error messages to debug it. Seems like there's something wrong with the inputs and variables but the messages aren't clear as to what's wrong with them.

When validating with womtool

[[email protected] five-dollar-genome-analysis-pipeline]$ java -jar ~/tools/womtool-34.jar validate germline_single_sample_workflow.wdl 
Exception in thread "main" scala.MatchError: null
    at wdl.draft2.model.WdlExpression$.toString(WdlExpression.scala:117)
    at wdl.draft2.model.WdlExpression$.toString(WdlExpression.scala:122)
    at wdl.draft2.model.WdlExpression.toString(WdlExpression.scala:200)
    at wdl.draft2.model.WdlExpression.toWomString(WdlExpression.scala:203)
    at wom.values.WomValue.valueString(WomValue.scala:49)
....

When running with cromwell

[2018-09-07 20:56:29,94] [error] WorkflowManagerActor Workflow 78794004-e040-49a7-903b-bad3f154b859 failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
null
wdl.draft2.model.WdlExpression$.toString(WdlExpression.scala:117)
wdl.draft2.model.WdlExpression$.toString(WdlExpression.scala:122)
wdl.draft2.model.WdlExpression.toString(WdlExpression.scala:200)
wdl.draft2.model.WdlExpression.toWomString(WdlExpression.scala:203)
wom.values.WomValue.valueString(WomValue.scala:49)
wom.values.WomValue.valueString$(WomValue.scala:49)
....
Post edited by bshifaw on

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