pairgenomealign/assets/multiqc_config.yml at 78234db31f7591a1e9e19db7bd979db1828da698 · nf-core/pairgenomealign · GitHub

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report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/tree/dev"
  target="_blank">nf-core/pairgenomealign</a> analysis pipeline. For information about
  how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/dev/docs/output"
  target="_blank">documentation</a>.
report_section_order:
  "nf-core-pairgenomealign-methods-description":
    order: -1000
  software_versions:
    order: -1001
  "nf-core-pairgenomealign-summary":
    order: -1002

export_plots: true

disable_version_detection: true

custom_data:
  train:
    file_format: "tsv"
    section_name: "Training parameter statistics"
    plot_type: "table"
    headers:
      id:
        title: "ID"
        description: "target___query"
      substitution_percent_identity:
        title: "Substitution Percent Identity"
      "last -t":
        title: "Temperature"
        description: "Parameter for converting between scores and probability ratios.
          This affects the column ambiguity estimates. A score is converted to a probability
          ratio by this formula: exp(score / TEMPERATURE). The default value is 1/lambda,
          where lambda is the scale factor of the scoring matrix, which is calculated
          by the method of Yu and Altschul (YK Yu et al. 2003, PNAS 100(26):15688-93)."
      "last -a":
        title: "Gap existence"
        description: "Gap existence cost (lastal -a)"
      "last -b":
        title: "Gap extension"
        description: "Gap extension cost (lastal -b)"
      "last -A":
        title: "Insertion existence"
        description: "Insertion existence cost (lastal -A)"
      "last -B":
        title: "Insertion extension"
        description: "Insertion extension cost (lastal -B)"
  last_o2o:
    file_format: "tsv"
    section_name: "Alignment statistics"
    plot_type: "table"
    headers:
      id:
        title: "ID"
        description: "target__query"
      TotalAlignmentLength:
        title: "Total alignment length"
      PercentIdentity:
        title: "Percent identity"
        description: "Matches / alignment length, including gaps"
      PercentIdentityNoGaps:
        title: "Ungapped percent identity"
        description: "Matches / (Matches + Mismatches), thus excluding gaps"

sp:
  last_o2o:
    fn: "*o2o_aln.tsv"
  train:
    fn: "*train.tsv"