cwl/helper/not-in-use/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 inputs:
  13   bam: File
  14   sample: string
  15
  16 outputs:
  17   out:
  18     type: File
  19     outputBinding:
  20       glob: "*sorted.bam"
  21
  22 baseCommand: samtools
  23
  24 arguments:
  25   - sort
  26   - -t
  27   - $(runtime.cores)
  28   - $(inputs.bam)
  29   - -o
  30   - $(runtime.outdir)/$(inputs.sample).sorted.bam