src/preprocessing/cwl/createSingleBam.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 $namespaces:
   4   arv: "http://arvados.org/cwl#"
   5   cwltool: "http://commonwl.org/cwltool#"
   6
   7 requirements:
   8   - class: DockerRequirement
   9     dockerPull: curii/bam2fastq
  10   - class: ShellCommandRequirement
  11
  12 hints:
  13   ResourceRequirement:
  14     ramMin: 4000
  15     coresMin: 1
  16     tmpdirMin: 150000
  17   arv:RuntimeConstraints:
  18     outputDirType: keep_output_dir
  19
  20 inputs:
  21   tarzipbam: File
  22   samplename: string
  23
  24 outputs:
  25   fastqs:
  26     type: File[]
  27     outputBinding:
  28       glob: "*fastq"
  29
  30 arguments:
  31   - tar
  32   - prefix: "-xvf"
  33     valueFrom: $(inputs.tarzipbam.path)
  34   - prefix: "-C"
  35     valueFrom: $(runtime.tmpdir)
  36   - {valueFrom: '&&', shellQuote: false}
  37   - samtools
  38   - merge
  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}
  44   - prefix: "-o"
  45     valueFrom: $(inputs.samplename)_R#.fastq