4 arv: "http://arvados.org/cwl#"
5 cwltool: "http://commonwl.org/cwltool#"
8 - class: DockerRequirement
9 dockerPull: curii/bam2fastq
10 - class: ShellCommandRequirement
17 arv:RuntimeConstraints:
18 outputDirType: keep_output_dir
33 valueFrom: $(inputs.tarzipbam.path)
35 valueFrom: $(runtime.tmpdir)
36 - {valueFrom: '&&', shellQuote: false}
39 - {valueFrom: $(runtime.tmpdir)/$(inputs.samplename).bam, shellQuote: false}
40 - {valueFrom: $(runtime.tmpdir)/*.bam, shellQuote: false}
41 - {valueFrom: '&&', shellQuote: false}
42 - /bam2fastq/bam2fastq
43 - {valueFrom: $(runtime.tmpdir)/$(inputs.samplename).bam, shellQuote: false}
45 valueFrom: $(inputs.samplename)_R#.fastq