I'm not sure if this is the correct spot for this question, as it lives somewhere in the Terra/GATK/Broad intersection, so please feel free to direct me elsewhere if needed.
I'm getting an error for some samples while running Funcotator in the Mutect2 featured workspace pipeline (https://github.com/broadinstitute/gatk/issues/6289). The latest version adds this helpful note in the returned error:
Job Mutect2.Funcotate:NA:3 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
I edited the wdl to to allow a value of 1 for continueOnReturnCode by changing the "standard_runtime" variable to include
"continueOnReturnCode": [0, 1]
per the instructions here, uploaded the new wdl to my workspace, and resubmitted a job that had previously failed, using the edited workflow.
Now, after the job is submitted, the status changes to "Aborting" and hangs. No error messages, no logs that I can check, no live objects in the Google bucket associated with the submission ID, and the status never moves to "Failed."
Would love any thoughts about how I might be able to troubleshoot this. Thanks!
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