#!/usr/bin/env cwl-runner

cwlVersion: v1.0

class: Workflow

requirements:
  - class: InlineJavascriptRequirement
  - class: StepInputExpressionRequirement
  - class: MultipleInputFeatureRequirement

inputs:
  job_uuid: string
  bam_path:
    type: File
    secondaryFiles: [^.bai]
  reference:
    type: File
    secondaryFiles: [.fai, ^.dict]
  known_indel1:
    type: File
    secondaryFiles: [.tbi]
  known_indel2:
    type: File
    secondaryFiles: [.tbi]
    
outputs:
  time_metrics_from_gatk3_leftalignindels:
    type: File
    outputSource: gatk3_leftalignindels/time_metrics
  time_metrics_from_gatk3_realignertargetcreator:
    type: File
    outputSource: gatk3_realignertargetcreator/time_metrics
  time_metrics_from_gatk3_indelrealigner:
    type: File
    outputSource: gatk3_indelrealigner/time_metrics
  harmonized_realigned_bam:
    type: File
    outputSource: gatk3_indelrealigner/realigned_bam

steps:
  gatk3_leftalignindels:
    run: ../../tools/realignment/gatk3_leftalignindels.cwl
    in:
      job_uuid: job_uuid
      bam_path: bam_path
      reference: reference
    out: [left_aligned_bam, time_metrics]

  gatk3_realignertargetcreator:
    run: ../../tools/realignment/gatk3_realignertargetcreator.cwl
    in:
      job_uuid: job_uuid
      bam_path: gatk3_leftalignindels/left_aligned_bam
      reference: reference
      known_indel1: known_indel1
      known_indel2: known_indel2
    out: [realigner_target, time_metrics]

  gatk3_indelrealigner:
    run: ../../tools/realignment/gatk3_indelrealigner.cwl
    in:
      job_uuid: job_uuid
      bam_path: gatk3_leftalignindels/left_aligned_bam
      reference: reference
      known_indel1: known_indel1
      known_indel2: known_indel2
      realigner_target: gatk3_realignertargetcreator/realigner_target
    out: [realigned_bam, time_metrics]