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