cwl/samtools-sort.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 requirements:
   5   DockerRequirement:
   6     dockerPull: curii/bwa-samtools-picard
   7   ShellCommandRequirement: {}
   8   ResourceRequirement:
   9     ramMin: 10000
  10     coresMin: 4
  11
  12 arguments:
  13   - samtools
  14   - sort
  15   - -t
  16   - $(runtime.cores)
  17   - $(inputs.bam)
  18   - -o
  19   - $(runtime.outdir)/$(inputs.sample).sorted.bam
  20
  21 inputs:
  22   bam: File
  23   sample: string
  24
  25 outputs:
  26   out:
  27     type: File
  28     outputBinding:
  29       glob: "*sorted.bam"