RNA-Seq/cwl/helper/samtools_index.cwl

   1 #!/usr/bin/env cwl-runner
   2 cwlVersion: v1.0
   3 class: CommandLineTool
   4
   5 doc: |
   6   Indexing BAM.
   7
   8 requirements:
   9   InitialWorkDirRequirement:
  10     listing:
  11       - $(inputs.bam_sorted)
  12 hints:
  13   ResourceRequirement:
  14     coresMin: 1
  15     ramMin: 20000
  16   DockerRequirement:
  17     dockerPull: quay.io/biocontainers/samtools:1.14--hb421002_0
  18
  19 baseCommand: ["samtools", "index"]
  20 arguments:
  21   - valueFrom: -b  # specifies that index is created in bai format
  22     position: 1
  23
  24 inputs:
  25   bam_sorted:
  26     doc: sorted bam input file
  27     type: File
  28     inputBinding:
  29       position: 2
  30
  31 outputs:
  32   bam_sorted_indexed:
  33     type: File
  34     secondaryFiles: .bai
  35     outputBinding:
  36       glob: $(inputs.bam_sorted.basename)
  37