cwl-test-file

class: Workflow
cwlVersion: v1.0
inputs:
  - id: transcripts
    type: 'File[]'
    'sbg:x': 0
    'sbg:y': 53.5
  - id: reads
    type: 'File[]'
    'sbg:x': 138.109375
    'sbg:y': 0
outputs:
  - id: quants
    outputSource:
      - quantifying/quantification
    type: File
    'sbg:x': 518.3233642578125
    'sbg:y': 53.5
steps:
  - id: indexing
    in:
      - id: fasta-files
        source:
          - transcripts
    out:
      - id: index
    run: ../tools/kallisto-index.cwl
    'sbg:x': 138.109375
    'sbg:y': 107
  - id: quantifying
    in:
      - id: index
        source:
          - indexing/index
      - id: fastqs
        source:
          - reads
    out:
      - id: quantification
    run: ../tools/kallisto-quant.cwl
    'sbg:x': 312.28125
    'sbg:y': 46.5
hints:
  - dockerPull: insilicodb/kallisto
    undefined: DockerRequirement