3 label: Germline variant calling using GATK with output gvcf
6 arv: "http://arvados.org/cwl#"
7 cwltool: "http://commonwl.org/cwltool#"
11 dockerPull: broadinstitute/gatk:4.1.7.0
14 arv:RuntimeConstraints:
15 outputDirType: keep_output_dir
46 baseCommand: /gatk/gatk
53 valueFrom: $(inputs.reference)
55 valueFrom: $(inputs.bam)
57 valueFrom: $(inputs.intervallist)
59 valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz