requirements:
DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
- InitialWorkDirRequirement:
- listing:
- - $(inputs.bam)
hints:
arv:RuntimeConstraints:
format: edam:format_2572 # BAM
label: Recalibrated BAM for given interval
secondaryFiles:
- - .bai
+ - ^.bai
outputBinding:
glob: "*nodups_BQSR.bam"
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "-I"
- valueFrom: $(inputs.bam.basename)
+ valueFrom: $(inputs.bam)
- prefix: "--bqsr-recal-file"
valueFrom: $(inputs.recaltable)
- prefix: "-L"