3 label: Generating recalibration table for BQSR
6 arv: "http://arvados.org/cwl#"
7 cwltool: "http://commonwl.org/cwltool#"
11 dockerPull: broadinstitute/gatk:4.1.7.0
12 InitialWorkDirRequirement:
17 arv:RuntimeConstraints:
18 outputDirType: keep_output_dir
51 baseCommand: /gatk/gatk
58 valueFrom: $(inputs.reference)
60 valueFrom: $(inputs.bam.basename)
61 - prefix: "--known-sites"
62 valueFrom: $(inputs.knownsites1)
64 valueFrom: $(inputs.sample)_recal_data.table