preprocess-illumina.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
  ScatterFeatureRequirement: {}
  SubworkflowFeatureRequirement: {}
  MultipleInputFeatureRequirement: {}
  StepInputExpressionRequirement: {}
  InlineJavascriptRequirement: {}

inputs:
  illumina_accession: string
  hg38: File

steps:
  unpack_ref_genome:
    in:
      file: hg38
    out:
      - hg_38_fa
    run: ./tools/unpack_ref_db.cwl

  fetch_fastqs:
    in:
      sra_accession: illumina_accession
    out:
      - fastq_file_1
      - fastq_file_2
    run: ../bio-cwl-tools/sratoolkit/prefetch_fastq.cwl

  fastp:
    in:
      fastq1: fetch_fastqs/fastq_file_1
      fastq2: fetch_fastqs/fastq_file_2
    out:
      - out_fastq1
      - out_fastq2
      - html_report
      - json_report
    run: ../bio-cwl-tools/fastp/fastp.cwl

  multiqc:
    in:
      qc_files_array: fastp/json_report
    out:
      - multiqc_zip
      - multiqc_html
    run: ../bio-cwl-tools/multiqc/multiqc.cwl

  bwa_mem:
    in:
      Index: unpack_ref_genome/hg_38_fa
      InputFile:
        source: [fastp/out_fastq1, fastp/out_fastq2]
        valueFrom: |
          ${
            return self.filter(function(x){return x});
          }
        linkMerge: merge_flattened
      Threads:
        valueFrom: $(1)
    out:
      - reads_stdout
    run: ../bio-cwl-tools/bwa/BWA-Mem.cwl

  samtools_view:
    in:
      sam: bwa_mem/reads_stdout
    out:
      - bam
    run: ../bio-cwl-tools/samtools/samtools_view_sam2bam.cwl

  samtools_fastq:
    in:
     bam_sorted: samtools_view/bam
    out:
      - fastq
    run: ../bio-cwl-tools/samtools/samtools_fastq.cwl

  rename_multiqc_html:
    in:
      srcfile: multiqc/multiqc_html
      newname:
        source: illumina_accession
        valueFrom: $(self)_multiqc.html
    out:
      - outfile
    run: ../bio-cwl-tools/util/rename.cwl

  rename_multiqc_zip:
    in:
      srcfile: multiqc/multiqc_zip
      newname:
        source: illumina_accession
        valueFrom: $(self)_multiqc.zip
    out:
      - outfile
    run: ../bio-cwl-tools/util/rename.cwl

  rename_fastp_html:
    in:
      srcfile: fastp/html_report
      newname:
        source: illumina_accession
        valueFrom: $(self)_fastp.html
    out:
      - outfile
    run: ../bio-cwl-tools/util/rename.cwl

  rename_fastp_json:
    in:
      srcfile: fastp/json_report
      newname:
        source: illumina_accession
        valueFrom: $(self)_fastp.json
    out:
      - outfile
    run: ../bio-cwl-tools/util/rename.cwl

  rename_bam:
    in:
      srcfile: samtools_view/bam
      newname:
        source: illumina_accession
        valueFrom: $(self).bam
    out:
      - outfile
    run: ../bio-cwl-tools/util/rename.cwl

outputs:
  original_fastq1:
    type: File
    format: edam:format_1930  # FASTQ
    outputSource: fetch_fastqs/fastq_file_1
  original_fastq2:
    type: File?
    format: edam:format_1930  # FASTQ
    outputSource: fetch_fastqs/fastq_file_2

  bam:
    type: File
    format: edam:format_2572  # BAM
    outputSource: rename_bam/outfile

  fastp_html_report:
    type: File
    format: edam:format_2331  # HTML
    outputSource: rename_fastp_html/outfile
  fastp_json_report:
    type: File
    format: edam:format_3464  # JSON
    outputSource: rename_fastp_json/outfile

  multiqc_html:
    type: File
    format: edam:format_2331  # HTML
    outputSource: rename_multiqc_html/outfile
  multiqc_zip:
    type: File
    format: edam:format_3464  # JSON
    outputSource: rename_multiqc_zip/outfile

  mapped_fastq:
    type: File
    format: edam:format_1930  # FASTQ
    outputSource: samtools_fastq/fastq

$namespaces:
  edam: http://edamontology.org/

$schemas:
  - http://edamontology.org/EDAM_1.20.owl