cwl/samtools-index.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 $namespaces:
   5   arv: "http://arvados.org/cwl#"
   6   cwltool: "http://commonwl.org/cwltool#"
   7
   8 requirements:
   9   DockerRequirement:
  10     dockerPull: curii/bwa-samtools-picard
  11   InitialWorkDirRequirement:
  12     listing:
  13       - $(inputs.bam)
  14
  15 hints:
  16   arv:RuntimeConstraints:
  17     outputDirType: keep_output_dir
  18
  19 inputs:
  20   bam: File
  21
  22 outputs:
  23   out:
  24     type: File
  25     outputBinding:
  26       glob: "*bam"
  27     secondaryFiles:
  28       - .bai
  29
  30 baseCommand: samtools
  31
  32 arguments:
  33   - index
  34   - $(inputs.bam.basename)