# fastqc.cwl
cwlVersion: v1.2
class: CommandLineTool
baseCommand: fastqc

inputs:
  fastq:
    type: File
    inputBinding:
      position: 1

outputs:
  html:
    type: File
    outputBinding:
      glob: "*_fastqc.html"
  zip:
    type: File
    outputBinding:
      glob: "*_fastqc.zip"

# bwa_mem.cwl
cwlVersion: v1.2
class: CommandLineTool
baseCommand: [bwa, mem]

requirements:
  DockerRequirement:
    dockerPull: biocontainers/bwa:v0.7.17
  ResourceRequirement:
    coresMin: 8
    ramMin: 16000

inputs:
  threads:
    type: int
    default: 8
    inputBinding:
      prefix: -t
      position: 1
  reference:
    type: File
    secondaryFiles:
      - .amb
      - .ann
      - .bwt
      - .pac
      - .sa
    inputBinding:
      position: 2
  reads_1:
    type: File
    inputBinding:
      position: 3
  reads_2:
    type: File?
    inputBinding:
      position: 4

stdout: aligned.sam

outputs:
  sam:
    type: stdout

# rnaseq.cwl
cwlVersion: v1.2
class: Workflow

inputs:
  fastq_1: File
  fastq_2: File
  salmon_index: Directory

outputs:
  quant_results:
    type: Directory
    outputSource: salmon/quant_dir

steps:
  fastp:
    run: fastp.cwl
    in:
      reads_1: fastq_1
      reads_2: fastq_2
    out: [trimmed_1, trimmed_2, json_report]

  salmon:
    run: salmon_quant.cwl
    in:
      index: salmon_index
      reads_1: fastp/trimmed_1
      reads_2: fastp/trimmed_2
    out: [quant_dir]

cwlVersion: v1.2
class: Workflow

requirements:
  ScatterFeatureRequirement: {}

inputs:
  fastq_files:
    type: File[]
  reference: File

outputs:
  bam_files:
    type: File[]
    outputSource: align/bam

steps:
  align:
    run: bwa_mem.cwl
    scatter: fastq
    in:
      fastq: fastq_files
      reference: reference
    out: [bam]

requirements:
  ScatterFeatureRequirement: {}
  MultipleInputFeatureRequirement: {}

steps:
  align:
    run: bwa_mem.cwl
    scatter: [reads_1, reads_2]
    scatterMethod: dotproduct
    in:
      reads_1: fastq_1_array
      reads_2: fastq_2_array
      reference: reference
    out: [bam]

# job.yaml
fastq_1:
  class: File
  path: data/sample1_R1.fq.gz
fastq_2:
  class: File
  path: data/sample1_R2.fq.gz
salmon_index:
  class: Directory
  path: ref/salmon_index
threads: 8

inputs:
  bam:
    type: File
    secondaryFiles:
      - .bai
  reference:
    type: File
    secondaryFiles:
      - pattern: .fai
        required: true
      - pattern: .dict
        required: false

requirements:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/salmon:1.10.0--h7e5ed60_0

hints:
  SoftwareRequirement:
    packages:
      salmon:
        version: ["1.10.0"]

# Run with Docker
cwltool --docker workflow.cwl job.yaml

# Run with Singularity
cwltool --singularity workflow.cwl job.yaml

requirements:
  ResourceRequirement:
    coresMin: 4
    coresMax: 16
    ramMin: 8000
    ramMax: 32000
    outdirMin: 10000
    tmpdirMin: 10000

cwlVersion: v1.2
class: Workflow

requirements:
  InlineJavascriptRequirement: {}

inputs:
  run_qc: boolean
  fastq: File

steps:
  fastqc:
    run: fastqc.cwl
    when: $(inputs.run_qc)
    in:
      run_qc: run_qc
      fastq: fastq
    out: [html]

# main.cwl
steps:
  qc_workflow:
    run: subworkflows/qc.cwl
    in:
      reads_1: fastq_1
      reads_2: fastq_2
    out: [qc_report, trimmed_1, trimmed_2]

  alignment_workflow:
    run: subworkflows/align.cwl
    in:
      reads_1: qc_workflow/trimmed_1
      reads_2: qc_workflow/trimmed_2
    out: [bam]

inputs:
  bam_files:
    type: File[]
  output_dir:
    type: string
    default: "results"

outputs:
  results:
    type: Directory
    outputBinding:
      glob: $(inputs.output_dir)

requirements:
  InlineJavascriptRequirement: {}

inputs:
  sample_name: string

outputs:
  output_bam:
    type: File
    outputBinding:
      glob: $(inputs.sample_name + ".sorted.bam")

arguments:
  - prefix: -o
    valueFrom: $(inputs.sample_name).sorted.bam

requirements:
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.reference)
        writable: false
      - entryname: config.txt
        entry: |
          threads=$(inputs.threads)
          memory=$(inputs.memory)

# salmon_quant.cwl
cwlVersion: v1.2
class: CommandLineTool
baseCommand: [salmon, quant]

requirements:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/salmon:1.10.0--h7e5ed60_0
  ResourceRequirement:
    coresMin: 8
    ramMin: 16000

inputs:
  index:
    type: Directory
    inputBinding:
      prefix: -i
  reads_1:
    type: File
    inputBinding:
      prefix: "-1"
  reads_2:
    type: File
    inputBinding:
      prefix: "-2"
  lib_type:
    type: string
    default: A
    inputBinding:
      prefix: -l
  threads:
    type: int
    default: 8
    inputBinding:
      prefix: --threads
  output_dir:
    type: string
    default: quant_output
    inputBinding:
      prefix: -o

outputs:
  quant_dir:
    type: Directory
    outputBinding:
      glob: $(inputs.output_dir)

# Validate CWL file
cwltool --validate workflow.cwl

# Run workflow
cwltool workflow.cwl job.yaml

# Run with Docker
cwltool --docker workflow.cwl job.yaml

# Run with Singularity
cwltool --singularity workflow.cwl job.yaml

# Run with caching
cwltool --cachedir ./cache workflow.cwl job.yaml

# Run on Toil
toil-cwl-runner workflow.cwl job.yaml