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 arguments:
  12   - samtools
  13   - index
  14   - $(inputs.bam.basename)
  15
  16 inputs:
  17   bam: File
  18
  19 outputs:
  20   out:
  21     type: File
  22     outputBinding:
  23       glob: "*bam"
  24     secondaryFiles:
  25       - .bai
  26