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/1.1.1" 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/1.1.1/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

export_plots: true

run_modules:
  - fastqc
  - qualimap
  - picard
  - mosdepth

module_order:
  - fastqc:
      name: "FastQC"
      path_filters:
        - "*.zip"
  - picard:
      name: "Picard"
  - qualimap:
      name: "Qualimap"
  - mosdepth:
      name: "Mosdepth"

extra_fn_clean_exts:
  - "_sorted_md"
  - type: regex
    pattern: "_T[0-9]"
