3 label: Applying base quality score recalibration
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 glob: "*nodups_BQSR.bam"
53 baseCommand: /gatk/gatk
60 valueFrom: $(inputs.reference)
62 valueFrom: $(inputs.bam.basename)
63 - prefix: "--bqsr-recal-file"
64 valueFrom: $(inputs.recaltable)
66 valueFrom: $(inputs.intervallist)
68 valueFrom: $(inputs.sample)nodups_BQSR.bam