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.

Workflow validates/runs when submitted alone, fails validation/doesnt run when used as a subworkflow

jsotojsoto Broad InstituteMember, Broadie, Dev ✭✭

It seems like this has to do with cromwell functions liek size and length failing validation when used as a subworkflow. This example was simplified to only having a length example but I saw similar things with size.

wm0eb-41f:revert_sam jsoto$ java -jar ~/Downloads/wdltool-0.14.jar validate InterestingSubWorkflow.wdl 

wm0eb-41f:revert_sam jsoto$ java -jar ~/Downloads/wdltool-0.14.jar validate Reanalysis.wdl 

ERROR: Missing value or call: Couldn't find value or call with name 'CreateSequenceGroupingTSV' in workflow (line 46):

  Int num_of_bqsr_scatters = length(CreateSequenceGroupingTSV.sequence_grouping)

It also fails in the same way when trying to run it on cromwell 29

The relevant workflows are attached.

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