-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