raredisease/assets/multiqc_config.yml at d8a2ec09e468fad421878a95e1380a6a30c6c794 · nf-core/raredisease · GitHub

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custom_logo: "nf-core-raredisease_logo_light.png"
custom_logo_url: https://github.com/nf-core/raredisease/
custom_logo_title: "nf-core/raredisease"
report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/raredisease/tree/dev"
  target="_blank">nf-core/raredisease</a> analysis pipeline. For information about
  how to interpret these results, please see the <a href="https://nf-co.re/raredisease/dev/docs/output"
  target="_blank">documentation</a>.
report_section_order:
  "nf-core-raredisease-methods-description":
    order: -1000
  software_versions:
    order: -1001
  "nf-core-raredisease-summary":
    order: -1002
  gatk_contamination:
    order: 1050
export_plots: true
run_modules:
  - fastqc
  - fastp
  - haplocheck
  - qualimap
  - picard
  - mosdepth
  - ngsbits
  - peddy
  - verifybamid
  - custom_content
module_order:
  - fastqc:
      name: "FastQC"
      path_filters:
        - "*.zip"
  - picard:
      name: "Picard"
  - qualimap:
      name: "Qualimap"
  - fastp:
      name: "fastp"
  - mosdepth:
      name: "Mosdepth"
  - haplocheck:
      name: "haplocheck"
  - ngsbits:
      name: "ngsbits"
  - peddy:
      name: "Peddy"
  - verifybamid:
      name: "VerifyBamID2"

# Custom content configuration for GATK contamination
custom_data:
  gatk_contamination:
    id: "gatk_contamination"
    section_name: "GATK Contamination"
    description: "Sample contamination estimates from GATK CalculateContamination based on common variant allele frequencies"
    plot_type: "generalstats"
    pconfig:
      contamination_pct:
        title: "Contamination"
        description: "Estimated sample contamination percentage"
        max: 10
        min: 0
        scale: "RdYlGn-rev"
        suffix: "%"
        format: "{:,.2f}"
        shared_key: "contamination"

# Make contamination visible in general stats by default
table_columns_visible:
  gatk_contamination:
    contamination_pct: true

# Color coding thresholds for contamination
table_cond_formatting_rules:
  contamination_pct:
    pass:
      - s_eq: "pass"
      - lt: 2.0
    warn:
      - s_eq: "warn"
      - lt: 5.0
      - gte: 2.0
    fail:
      - s_eq: "fail"
      - gte: 5.0

# Add to General Statistics table configuration
table_columns_placement:
  gatk_contamination:
    contamination_pct: 900

extra_fn_clean_exts:
  - "_sorted_md"
  - "_contamination"
  - "_pileups"
  - type: regex
    pattern: "_LNUMBER[0-9]{1,}"

disable_version_detection: true