mixcr.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: mgibio/mixcr
  SoftwareRequirement:
    packages:
      mixcr:
        specs: [ 'https://doi.org/10.1038/nmeth.3364' ]

inputs:
  reads_left:
    type: File
    inputBinding:
      position: 1

  reads_right:
    type: File
    inputBinding:
      position: 2

baseCommand:
  - mixcr
  - align

arguments:
  - valueFrom: $(inputs.reads_left.basename).vdjca
    position: 3
  - valueFrom: $(inputs.reads_left.basename).report.txt
    prefix: --report

outputs:
  alignments:
    type: File
    outputBinding:
      glob: $(inputs.reads_left.basename).vdjca

  report:
    type: File
    outputBinding:
      glob: $(inputs.reads_left.basename).report.txt

wget http://files.milaboratory.com/mixcr/paper/real_trb.zip
unzip real_trb.zip
cwltool mixcr.cwl  --reads_left true_trb_R1.fastq.gz --reads_right true_trb_R2.fastq.gz