class: Workflow
cwlVersion: v1.0
id: aggregate_visualize
label: aggregate_visualize
$namespaces:
  sbg: 'https://www.sevenbridges.com/'
inputs:
  - id: duplex_extraction_files
    type: 'File[]'
  - id: collapsed_extraction_files
    type: 'File[]'
  - id: uncollapsed_bam_stats_pool_a_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: simplex_bam_pool_b_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: simplex_bam_pool_a_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: gatk_mean_quality_by_cycle_recal_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: duplex_bam_stats_pool_b_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: duplex_bam_stats_pool_a_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: collapsed_bam_stats_pool_b_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: collapsed_bam_stats_pool_a_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: collapsed_bam_duplex_metrics_pool_b_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: collapsed_bam_duplex_metrics_pool_a_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: samples-json
    type: File
  - id: config
    type: File?
  - id: duplex_bam_sequence_qc_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
  - id: uncollapsed_bam_stats_pool_b_dir
    type:
      type: array
      items:
        - File
        - Directory
        - 'null'
outputs:
  - id: multiqc_zip
    outputSource:
      - multiqc_1_10_1/multiqc_zip
    type: File?
  - id: multiqc_html
    outputSource:
      - multiqc_1_10_1/multiqc_html
    type: File
  - id: multiqc_output_dir
    outputSource:
      - multiqc_1_10_1/multiqc_output_dir
    type: Directory
steps:
  - id: qc_aggregator
    in:
      - id: duplex_extraction_files
        source:
          - duplex_extraction_files
      - id: simplex_bam_pool_a_dir
        source:
          - simplex_bam_pool_a_dir
      - id: simplex_bam_pool_b_dir
        source:
          - simplex_bam_pool_b_dir
      - id: duplex_bam_sequence_qc_dir
        source:
          - duplex_bam_sequence_qc_dir
      - id: duplex_bam_stats_pool_a_dir
        source:
          - duplex_bam_stats_pool_a_dir
      - id: duplex_bam_stats_pool_b_dir
        source:
          - duplex_bam_stats_pool_b_dir
      - id: collapsed_bam_stats_pool_a_dir
        source:
          - collapsed_bam_stats_pool_a_dir
      - id: collapsed_bam_stats_pool_b_dir
        source:
          - collapsed_bam_stats_pool_b_dir
      - id: collapsed_bam_duplex_metrics_pool_a_dir
        source:
          - collapsed_bam_duplex_metrics_pool_a_dir
      - id: collapsed_bam_duplex_metrics_pool_b_dir
        source:
          - collapsed_bam_duplex_metrics_pool_b_dir
      - id: gatk_mean_quality_by_cycle_recal_dir
        source:
          - gatk_mean_quality_by_cycle_recal_dir
      - id: uncollapsed_bam_stats_pool_b_dir
        source:
          - uncollapsed_bam_stats_pool_b_dir
      - id: uncollapsed_bam_stats_pool_a_dir
        source:
          - uncollapsed_bam_stats_pool_a_dir
      - id: collapsed_extraction_files
        source:
          - collapsed_extraction_files
    out:
      - id: aggregate_qc_stats
    run: qc_aggregator/qc_aggregator.cwl
    label: qc_aggregator
  - id: general_stats_parse
    in:
      - id: directory
        source: qc_aggregator/aggregate_qc_stats
      - id: samples-json
        source: samples-json
      - id: config
        source: config
    out:
      - id: aggregate_parsed_stats
    run: cwl-commandlinetools/access_utils/0.1.1/general_stats_parse.cwl
    label: general_stats_parse
  - id: multiqc_1_10_1
    in:
      - id: qc_files_dir
        source: general_stats_parse/aggregate_parsed_stats
      - id: config
        source: config
    out:
      - id: multiqc_output_dir
      - id: multiqc_html
      - id: multiqc_zip
    run: cwl-commandlinetools/multiqc/1.10.1.7/multiqc.cwl
requirements:
  - class: SubworkflowFeatureRequirement