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:
21 arv:RuntimeConstraints:
22 outputDirType: keep_output_dir
46 baseCommand: /gatk/gatk
53 valueFrom: $(inputs.gvcf1.basename)
55 valueFrom: $(inputs.gvcf2.basename)
57 valueFrom: $(inputs.sample)g.vcf.gz