3 label: Gathering vcf using Picard
5 arv: "http://arvados.org/cwl#"
6 cwltool: "http://commonwl.org/cwltool#"
10 dockerPull: broadinstitute/gatk:4.1.7.0
11 ShellCommandRequirement: {}
12 InitialWorkDirRequirement:
22 arv:RuntimeConstraints:
23 outputDirType: keep_output_dir
49 baseCommand: /gatk/gatk
56 valueFrom: $(inputs.gvcflist.basename)
58 valueFrom: $(inputs.sample)g.vcf.gz