cromwell is skipping a scatter call
I am trying to run the wdl workflow file for germline CNVCaller cohort mode.
After modifying the original file from the github repository to run it locally on our servers, I faced the following issues:
- If I provide the .json input file with the optional inputs untouched, I get a message of "no coercion defined" for all of the optional parameters, and the workflow stops.
- I could work around this issue by entering the default parameters directly in the wdl code.
- After the "DetermineGermlineContigPloidyCohortMode" call was complete, the pipeline goes directly to "CNVTasks.PostprocessGermlineCNVCalls" call, skipping the "GermlineCNVCallerCohortMode" call and its preceeding scatter step; I then get an error of 'calls-shard-path' is required, which is the expected output of the "GermlineCNVCallerCohortMode" uncalled step.
I wonder why this step is being skipped, although it is called in order?