cwl/helper/not-in-use/samtools-fixmate.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 $namespaces:
   5   arv: "http://arvados.org/cwl#"
   6   cwltool: "http://commonwl.org/cwltool#"
   7
   8 requirements:
   9   DockerRequirement:
  10     dockerPull: curii/bwa-samtools-picard
  11   ShellCommandRequirement: {}
  12   ResourceRequirement:
  13     ramMin: 10000
  14     coresMin: 4
  15
  16 hints:
  17   arv:RuntimeConstraints:
  18     outputDirType: keep_output_dir
  19
  20 inputs:
  21   bam: File
  22   sample: string
  23
  24 outputs:
  25   out:
  26     type: File
  27     outputBinding:
  28       glob: "*fixed.bam"
  29
  30 baseCommand: samtools
  31
  32 arguments:
  33   - fixmate
  34   - -O
  35   - "bam"
  36   - $(inputs.bam.path)
  37   - $(runtime.outdir)/$(inputs.sample).fixed.bam