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

   1 #!/usr/bin/env cwl-runner
   2 cwlVersion: v1.0
   3 class: CommandLineTool
   4
   5 hints:
   6   DockerRequirement:
   7     dockerPull: biodckr/bwa
   8
   9 baseCommand: [bwa, mem]
  10
  11 arguments:
  12   - {prefix: "-t", valueFrom: $(runtime.cores)}
  13   - {prefix: "-R", valueFrom: "@RG\tID:$(inputs.group_id)\tPL:$(inputs.PL)\tSM:$(inputs.sample_id)"}
  14
  15 inputs:
  16   reference:
  17     type: File
  18     inputBinding:
  19       position: 1
  20       valueFrom: $(self.dirname)/$(self.nameroot)
  21     secondaryFiles:
  22       - ^.ann
  23       - ^.amb
  24       - ^.pac
  25       - ^.sa
  26     doc: The index files produced by `bwa index`
  27   read_p1:
  28     type: File
  29     inputBinding:
  30       position: 2
  31     doc: The reads, in fastq format.
  32   read_p2:
  33     type: File?
  34     inputBinding:
  35       position: 3
  36     doc:  For mate paired reads, the second file (optional).
  37   group_id: string
  38   sample_id: string
  39   PL: string
  40
  41 stdout: $(inputs.read_p1.nameroot).sam
  42
  43 outputs:
  44   aligned_sam:
  45     type: stdout