To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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

jsotojsoto Broad InstituteMember, Broadie

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.

Best Answer


Sign In or Register to comment.