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