WGS-processing/cwl/helper/samtools-sort.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Sorting Bam file
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7   cwltool: "http://commonwl.org/cwltool#"
   8
   9 requirements:
  10   DockerRequirement:
  11     dockerPull: curii/bwa-samtools-picard
  12   ShellCommandRequirement: {}
  13   ResourceRequirement:
  14     ramMin: 20000
  15     coresMin: 4
  16
  17 hints:
  18   arv:RuntimeConstraints:
  19     keep_cache: 9216
  20     outputDirType: keep_output_dir
  21
  22 inputs:
  23   bam: File
  24   sample: string
  25
  26 outputs:
  27   sortedbam:
  28     type: File
  29     outputBinding:
  30       glob: "*sorted.bam"
  31
  32 baseCommand: samtools
  33
  34 arguments:
  35   - sort
  36   - -@
  37   - $(runtime.cores)
  38   - $(inputs.bam.path)
  39   - -m
  40   - '2G'
  41   - -o
  42   - $(inputs.sample).sorted.bam