doc/user/cwl/bwa-mem/bwa-mem.cwl

   1 #!/usr/bin/env cwl-runner
   2 cwlVersion: draft-3
   3 class: CommandLineTool
   4
   5 hints:
   6   - class: DockerRequirement
   7     dockerPull: biodckr/bwa
   8 requirements:
   9   - class: InlineJavascriptRequirement
  10
  11 baseCommand: [bwa, mem]
  12
  13 arguments:
  14   - {prefix: "-t", valueFrom: $(runtime.cores)}
  15   - {prefix: "-R", valueFrom: "@RG\tID:$(inputs.group_id)\tPL:$(inputs.PL)\tSM:$(inputs.sample_id)"}
  16
  17 inputs:
  18   - id: reference
  19     type: File
  20     inputBinding:
  21       position: 1
  22       valueFrom: $(self.path.match(/(.*)\.[^.]+$/)[1])
  23     secondaryFiles:
  24       - ^.ann
  25       - ^.amb
  26       - ^.pac
  27       - ^.sa
  28     description: The index files produced by `bwa index`
  29   - id: read_p1
  30     type: File
  31     inputBinding:
  32       position: 2
  33     description: The reads, in fastq format.
  34   - id: read_p2
  35     type: ["null", File]
  36     inputBinding:
  37       position: 3
  38     description:  For mate paired reads, the second file (optional).
  39   - id: group_id
  40     type: string
  41   - id: sample_id
  42     type: string
  43   - id: PL
  44     type: string
  45
  46 stdout: $(inputs.read_p1.path.match(/\/([^/]+)\.[^/.]+$/)[1] + ".sam")
  47
  48 outputs:
  49   - id: aligned_sam
  50     type: File
  51     outputBinding:
  52       glob: $(inputs.read_p1.path.match(/\/([^/]+)\.[^/.]+$/)[1] + ".sam")