Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
requirements:
DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
- InitialWorkDirRequirement:
- listing:
- - $(inputs.bam)
hints:
arv:RuntimeConstraints:
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "-I"
- valueFrom: $(inputs.bam.basename)
+ valueFrom: $(inputs.bam)
- prefix: "--bqsr-recal-file"
valueFrom: $(inputs.recaltable)
- prefix: "-L"
requirements:
DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
- InitialWorkDirRequirement:
- listing:
- - $(inputs.bam)
hints:
arv:RuntimeConstraints:
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "-I"
- valueFrom: $(inputs.bam.basename)
+ valueFrom: $(inputs.bam)
- prefix: "--known-sites"
valueFrom: $(inputs.knownsites)
- prefix: "-L"