---
  class: "Workflow"
  cwlVersion: "v1.0"
  fdn_meta: 
    category: "align + filter + count"
    data_types: 
      - "Repli-seq"
    description: "This is a subworkflow of the Repli-seq data processing pipeline. It takes a raw fastq file, aligns to the reference genome, performs filtering and reports read counts in a bedgraph (bg) format."
    name: "repliseq-parta"
    title: "Repli-seq data processing pipeline for alignment, filtering and counting"
    workflow_type: "Repli-seq data processing"
  inputs: 
    - 
      fdn_format: "fastq"
      id: "#fastq"
      type: 
        - "File"
    - 
      fdn_format: "bwaIndex"
      id: "#bwaIndex"
      type: 
        - "File"
    - 
      fdn_format: "chromsizes"
      id: "#chromsizes"
      type: 
        - "File"
    - 
      default: 4
      id: "#nthreads"
      type: 
        - "int"
    - 
      default: "2G"
      id: "#memperthread"
      type: 
        - "string"
    - 
      default: 5000
      id: "#winsize"
      type: 
        - "int"
  outputs: 
    - 
      fdn_format: "bam"
      fdn_output_type: "processed"
      id: "#filtered_sorted_deduped_bam"
      outputSource: "#dedup/out_deduped_bam"
      type: 
        - "File"
    - 
      fdn_output_type: "QC"
      id: "#dedup_qc_report"
      outputSource: "#dedup/out_qc_report"
      type: 
        - "File"
    - 
      fdn_format: "bg"
      fdn_output_type: "processed"
      fdn_secondary_file_formats: 
        - "bg_px2"
        - "bw"
      id: "#count_bg"
      outputSource: "#count/out_count_bg"
      type: 
        - "File"
  requirements: 
    - 
      class: "InlineJavascriptRequirement"
  steps: 
    - 
      fdn_step_meta: 
        analysis_step_types: 
          - "adapter removal"
        description: "Adapter removal according to the Repli-seq pipeline"
        software_used: 
          - "cutadapt_1.14"
          - "repli-seq-pipeline_f69a459"
      id: "#clip"
      in: 
        - 
          arg_name: "input_fastq"
          fdn_cardinality: "single"
          fdn_format: "fastq"
          fdn_type: "data file"
          id: "#clip/input_fastq"
          source: "#fastq"
      out: 
        - 
          arg_name: "out_clipped_fastq"
          fdn_cardinality: "single"
          fdn_format: "fastq"
          id: "#clip/out_clipped_fastq"
      run: "clip.cwl"
    - 
      fdn_step_meta: 
        analysis_step_types: 
          - "alignment"
        description: "Alignment according to the Repli-seq pipeline"
        software_used: 
          - "bwa_0.7.15"
          - "repli-seq-pipeline_f69a459"
      id: "#align"
      in: 
        - 
          arg_name: "fastq1"
          fdn_cardinality: "single"
          fdn_format: "fastq"
          id: "#align/fastq1"
          source: "#clip/out_clipped_fastq"
        - 
          arg_name: "bwa_index"
          fdn_cardinality: "single"
          fdn_format: "bwaIndex"
          fdn_type: "reference file"
          id: "#align/bwa_index"
          source: "#bwaIndex"
        - 
          arg_name: "nThreads"
          fdn_cardinality: "single"
          fdn_type: "parameter"
          id: "#align/nThreads"
          source: "#nthreads"
      out: 
        - 
          arg_name: "out_bam"
          fdn_cardinality: "single"
          fdn_format: "bam"
          id: "#align/out_bam"
      run: "align.cwl"
    - 
      fdn_step_meta: 
        analysis_step_types: 
          - "filtering"
          - "sorting"
        description: "Filtering and sorting according to the Repli-seq pipeline"
        software_used: 
          - "samtools_1.4"
          - "repli-seq-pipeline_f69a459"
      id: "#filtersort"
      in: 
        - 
          arg_name: "input_bam"
          fdn_cardinality: "single"
          fdn_format: "bam"
          id: "#filtersort/input_bam"
          source: "#align/out_bam"
        - 
          arg_name: "nthreads"
          fdn_cardinality: "single"
          fdn_type: "parameter"
          id: "#filtersort/nthreads"
          source: "#nthreads"
        - 
          arg_name: "memperthread"
          fdn_cardinality: "single"
          fdn_type: "parameter"
          id: "#filtersort/memperthread"
          source: "#memperthread"
      out: 
        - 
          arg_name: "out_filtered_sorted_bam"
          fdn_cardinality: "single"
          fdn_format: "bam"
          id: "#filtersort/out_filtered_sorted_bam"
      run: "filtersort.cwl"
    - 
      fdn_step_meta: 
        analysis_step_types: 
          - "duplicate removal"
        description: "PCR Duplicate removal according to the Repli-seq pipeline"
        software_used: 
          - "samtools_1.4"
          - "repli-seq-pipeline_f69a459"
      id: "#dedup"
      in: 
        - 
          arg_name: "input_bam"
          fdn_cardinality: "single"
          fdn_format: "bam"
          id: "#dedup/input_bam"
          source: "#filtersort/out_filtered_sorted_bam"
      out: 
        - 
          arg_name: "out_deduped_bam"
          fdn_cardinality: "single"
          fdn_format: "bam"
          fdn_type: "data file"
          id: "#dedup/out_deduped_bam"
        - 
          arg_name: "out_qc_report"
          fdn_cardinality: "single"
          fdn_type: "QC"
          id: "#dedup/out_qc_report"
      run: "dedup.cwl"
    - 
      fdn_step_meta: 
        analysis_step_types: 
          - "binning"
          - "aggregation"
        description: "Read aggregation according to the Repli-seq pipeline"
        software_used: 
          - "bedtools_2.26.0"
          - "repli-seq-pipeline_f69a459"
          - "pairix_0.3.5"
          - "bedGraphToBigWig_v302.1.0"
      id: "#count"
      in: 
        - 
          arg_name: "input_bam"
          fdn_cardinality: "single"
          fdn_format: "bam"
          fdn_type: "data file"
          id: "#count/input_bam"
          source: "#dedup/out_deduped_bam"
        - 
          arg_name: "chrsizes"
          fdn_cardinality: "single"
          fdn_format: "chromsize"
          fdn_type: "reference file"
          id: "#count/chrsizes"
          source: "#chromsizes"
        - 
          arg_name: "winsize"
          fdn_cardinality: "single"
          fdn_type: "parameter"
          id: "#count/winsize"
          source: "#winsize"
      out: 
        - 
          arg_name: "out_count_bg"
          fdn_cardinality: "single"
          fdn_format: "bg"
          fdn_type: "data file"
          id: "#count/out_count_bg"
      run: "count.cwl"