cwl/samtools-sort.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   InitialWorkDirRequirement:
  13     listing:
  14       - $(inputs.bam)
  15   ResourceRequirement:
  16     ramMin: 20000
  17     coresMin: 4
  18
  19 hints:
  20   arv:RuntimeConstraints:
  21     keep_cache: 9216
  22     outputDirType: keep_output_dir
  23
  24 inputs:
  25   bam: File
  26   sample: string
  27
  28 outputs:
  29   out:
  30     type: File
  31     outputBinding:
  32       glob: "*sorted.bam"
  33
  34 baseCommand: samtools
  35
  36 arguments:
  37   - sort
  38   - -@
  39   - $(runtime.cores)
  40   - $(inputs.bam.basename)
  41   - -m
  42   - '2G'
  43   - -o
  44   - $(inputs.sample).sorted.bam