cwl/samtools-index.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 requirements:
   5   DockerRequirement:
   6     dockerPull: curii/bwa-samtools-picard
   7   InitialWorkDirRequirement:
   8     listing:
   9       - $(inputs.bam)
  10
  11 inputs:
  12   bam: File
  13
  14 outputs:
  15   out:
  16     type: File
  17     outputBinding:
  18       glob: "*bam"
  19     secondaryFiles:
  20       - .bai
  21
  22 baseCommand: samtools
  23
  24 arguments:
  25   - index
  26   - $(inputs.bam.basename)