We observed an inconsistent but reoccurring issue in which GenotypeBatch.GenotypeDepthPart2 failed in Terra with the error message Workflow is making no progress but has the following unstarted job keys: [...]. This issue is sometimes solved by re-running the workflow, but not always. It appears to be a cromwell bug but we hypothesize that it is related to the empty scatter over variants <5kb in length. As a workaround, I added a check to see if there were variants <5kb before scattering.
Testing
Validated all WDLs and JSONs with womtool and Terra validation script
Tested in GREGoR cohort where this issue appeared repeatedly. All batches succeeded
Updates
We observed an inconsistent but reoccurring issue in which GenotypeBatch.GenotypeDepthPart2 failed in Terra with the error message
Workflow is making no progress but has the following unstarted job keys: [...]. This issue is sometimes solved by re-running the workflow, but not always. It appears to be a cromwell bug but we hypothesize that it is related to the empty scatter over variants <5kb in length. As a workaround, I added a check to see if there were variants <5kb before scattering.Testing