fastq2bam.cwl.yaml

class: Workflow
cwlVersion: v1.0
label: MC3-E2E

requirements:
  - class: MultipleInputFeatureRequirement
  - class: SubworkflowFeatureRequirement
  - class: ScatterFeatureRequirement
  - class: StepInputExpressionRequirement
  - class: InlineJavascriptRequirement

inputs:
  tumor_fastqs:
    - type: array
      items: File

  tumor_sample_name:
    type: string

  normal_fastqs:
    - type: array
      items: File

  normal_sample_name:
    type: string

  dbsnp:
    type: File
    secondaryFiles:
      - .tbi

  1000g_phase1:
    type: File
    secondaryFiles:
      - .tbi
  
  mills_and_1000g:
    type: File
    secondaryFiles:
      - .tbi

  referenceTar:
    type: File
    doc: "The core reference (fa, fai, dict) as tar.gz"

  reference:
    type: File
    secondaryFiles:
      - .fai
      - ^.dict

  bwa_idx:
    type: File
    doc: "The BWA indexes in tar.gz"

steps:
  align_tumor:
    run: dockstore-cgpmap/Dockstore.cwl
    in:
      bams_in: tumor_fastqs
      cram:
        default: false
      sample: tumor_sample_name
      reference: referenceTar
      bwa_idx: bwa_idx
    out:
      - out_bam

  align_normal:
    run: dockstore-cgpmap/Dockstore.cwl
    in:
      bams_in: normal_fastqs
      cram:
        default: false
      sample: normal_sample_name
      reference: referenceTar
      bwa_idx: bwa_idx
    out:
      - out_bam

  gatk_coclean:
    run: gatk-cocleaning-tool/gatk-cocleaning-workflow.cwl.yaml
    in:
      tumor_bam: align_tumor/out_bam
      normal_bam: align_normal/out_bam
      knownIndels:
        - 1000g_phase1
        - mills_and_1000g
      knownSites:
        source: dbsnp
        valueFrom: ${ return [ self ]; }
      reference: reference
    out:
      - cleaned_tumor_bam
      - cleaned_normal_bam

  rename_tumor_index:
    run: rename.cwl.yaml
    in:
      in_file: gatk_coclean/cleaned_tumor_bam
    out:
      - out_file

  rename_normal_index:
    run: rename.cwl.yaml
    in:
      in_file: gatk_coclean/cleaned_normal_bam
    out:
      - out_file

outputs:
  normalBam:
    type: File
    outputSource: gatk_coclean/cleaned_normal_bam
  tumorBam:
    type: File
    outputSource: gatk_coclean/cleaned_tumor_bam