5 arv: "http://arvados.org/cwl#"
6 cwltool: "http://commonwl.org/cwltool#"
10 dockerPull: broadinstitute/gatk:4.1.7.0
13 arv:RuntimeConstraints:
14 outputDirType: keep_output_dir
43 baseCommand: /gatk/gatk
50 valueFrom: $(inputs.reference)
51 - prefix: "--remove-unused-alternates"
54 valueFrom: $(inputs.gvcf.path)
56 valueFrom: selected$(inputs.gvcf.basename)