Demo

tool.test.json

{
  "input_normal": {
    "path": "normal.bam",
    "class": "File"
  },
  "input_tumour": {
    "path": "tumour.bam",
    "class": "File"
  },
  "index": {
    "path": "mutect_smallindex",
    "class": "Directory"
  },
  "ncpus": 12,
  "out_vcf": "dmutations.vcf"
}

tool.yaml

cwlVersion: v1.0
class: CommandLineTool

doc: "example tool"

hints:
  DockerRequirement:
    dockerPull: ubuntu 


requirements:
  - class: InlineJavascriptRequirement

inputs:

  input_normal:
    type: File
    doc: |
      bam input for control
    inputBinding:
      position: 1 
    secondaryFiles:
      - .bai

  input_tumour:
    type: File
    doc: |
      bam input for tumour
    inputBinding:
      position: 2 
    secondaryFiles:
      - .bai


outputs:
  mutations:
    type: File
    outputBinding:
      glob: test.vcf


baseCommand: ["cat"]

arguments: 
  - valueFrom: $(inputs.input_normal.path + ".bai")
  - valueFrom: $(inputs.input_tumour.path + ".bai")

stdout: test.vcf

workflow.cwl

#!/usr/bin/env cwl-runner

class: Workflow
cwlVersion: v1.0

doc: "example workflow"

requirements:
  - class: MultipleInputFeatureRequirement

inputs: 

  TUMOUR_BAM: 
    type: File

  NORMAL_BAM: 
    type: File

outputs:

  OUTPUT:
    type: File
    outputSource: mutect/mutations

steps:

  mutect:
    run: tool.cwl
    in:
      input_normal: NORMAL_BAM 
      input_tumour: TUMOUR_BAM
    out: [mutations]

workflow.redundant.cwl

#!/usr/bin/env cwl-runner

class: Workflow
cwlVersion: v1.0

doc: "example workflow"

requirements:
  - class: MultipleInputFeatureRequirement

inputs: 

  TUMOUR_BAM: 
    type: File
    secondaryFiles:
      - .bai

  NORMAL_BAM: 
    type: File
    secondaryFiles:
      - .bai

outputs:

  OUTPUT:
    type: File
    outputSource: mutect/mutations

steps:

  mutect:
    run: tool.cwl
    in:
      input_normal: NORMAL_BAM 
      input_tumour: TUMOUR_BAM
    out: [mutations]

workflow.test.json

{
  "TUMOUR_BAM": {
    "path": "tumour.bam",
    "class": "File"
  },
  "NORMAL_BAM": {
    "path": "normal.bam",
    "class": "File"
  },
  "index": {
    "path": "mutect_smallindex",
    "class": "Directory"
  },
  "ncpus": 12,
  "output": "dmutations.vcf"
}