WGS-processing/cwl/helper/samtools-index.cwl

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