3 label: Marking Duplicates using Picard
5 arv: "http://arvados.org/cwl#"
6 cwltool: "http://commonwl.org/cwltool#"
10 dockerPull: broadinstitute/gatk:4.1.7.0
16 arv:RuntimeConstraints:
17 outputDirType: keep_output_dir
33 baseCommand: /gatk/gatk
40 valueFrom: $(inputs.bam.path)
42 valueFrom: marked_dups$(inputs.bam.basename)
44 valueFrom: "metrics.txt"