+cwlVersion: v1.1
+class: CommandLineTool
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ - class: DockerRequirement
+ dockerPull: curii/bam2fastq
+ - class: ShellCommandRequirement
+
+hints:
+ ResourceRequirement:
+ ramMin: 4000
+ coresMin: 1
+ tmpdirMin: 150000
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+
+inputs:
+ tarzipbam: File
+ samplename: string
+
+outputs:
+ fastqs:
+ type: File[]
+ outputBinding:
+ glob: "*fastq"
+
+arguments:
+ - tar
+ - prefix: "-xvf"
+ valueFrom: $(inputs.tarzipbam.path)
+ - prefix: "-C"
+ valueFrom: $(runtime.tmpdir)
+ - {valueFrom: '&&', shellQuote: false}
+ - samtools
+ - merge
+ - {valueFrom: $(runtime.tmpdir)/$(inputs.samplename).bam, shellQuote: false}
+ - {valueFrom: $(runtime.tmpdir)/*.bam, shellQuote: false}
+ - {valueFrom: '&&', shellQuote: false}
+ - /bam2fastq/bam2fastq
+ - {valueFrom: $(runtime.tmpdir)/$(inputs.samplename).bam, shellQuote: false}
+ - prefix: "-o"
+ valueFrom: $(inputs.samplename)_R#.fastq