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Bug #22463

open

WGS-processing tutorial workflow fails because steps are missing expected outputs

Added by Brett Smith 3 months ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
Sample Pipelines
Target version:
-
Story points:
-

Description

At least when run with the provided yml/wgs-processing-wf-chr19.yml input. See tordo-xvhdp-hr5370pocazfy67 which logged these errors:

cwltool: [step mark-duplicates] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/bwamem-gatk-report-wf.cwl#mark-duplicates/dupbam
cwltool: [step mark-duplicates] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/bwamem-gatk-report-wf.cwl#mark-duplicates/dupmetrics
cwltool: [step mark-duplicates_3] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/bwamem-gatk-report-wf.cwl#mark-duplicates/dupbam
cwltool: [step mark-duplicates_3] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/bwamem-gatk-report-wf.cwl#mark-duplicates/dupmetrics
cwltool: [step applyBQSR] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/gatk-wf-with-interval.cwl#applyBQSR/recalbam
cwltool: [step gather-GVCFs_2] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/scatter-gatk-wf-with-interval.cwl#gather-GVCFs/gatheredgvcf
cwltool: [step gather-GVCFs] Output is missing expected field keep:fd9072b90bd15c2553a585824c66b93a+2900/helper/scatter-gatk-wf-with-interval.cwl#gather-GVCFs/gatheredgvcf
arvados.cwl-runner: Overall process status is permanentFail

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