report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/multiplesequencealign/releases/tag/1.0.0" target="_blank">nf-core/multiplesequencealign</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/multiplesequencealign/1.0.0/docs/output" target="_blank">documentation</a>.
report_section_order:
  "nf-core-multiplesequencealign-methods-description":
    order: -1000
  software_versions:
    order: -1001
  "nf-core-multiplesequencealign-summary":
    order: -1002

report_header_info:
  - Application Type: "Muliple Sequence Alignment deplyoment and benchmarking."

export_plots: true

disable_version_detection: true

run_modules:
  - custom_content

custom_data:
  summary_stats:
    id: "summary_stats"
    section_name: "Summary Stats"
    plot_type: "table"
    anchor: "summary_stats"
    namespace: "summary_stats"
    pconfig:
      id: "summary_stats"
      title: "Summary statistics"

custom_table_header_config:
  summary_stats:
    perc_sim:
      description: "Average percentage similarity between all sequences in the input fasta file."
      namespace: "Fasta"
      max: 100
      format: "{:,.2f}"
      suffix: "%"
    fasta:
      description: "Input fasta file."
      hidden: False
      namespace: "Fasta"
    n_sequences:
      description: "Number of sequences in the input fasta file."
      hidden: False
      namespace: "Fasta"
      scale: "Set2"
    seqlength_mean:
      description: "Average sequence length in the input fasta file."
      hidden: False
      namespace: "Fasta"
      format: "{:,.1f}"
    seqlength_max:
      description: "Maximum sequence length in the input fasta file."
      hidden: True
      namespace: "Fasta"
      format: "{:,.1f}"
    seqlength_median:
      description: "Median sequence length in the input fasta file."
      hidden: True
      namespace: "Fasta"
      format: "{:,.1f}"
    sp:
      description: "Sum of Pairs metric."
      hidden: False
      namespace: "Alignment"
      format: "{:,.1f}"
      max: 100
    tc:
      description: "Total Column metric."
      hidden: False
      namespace: "Alignment"
      format: "{:,.1f}"
      max: 100
    EVALUATED:
      description: "EVALUATED metric."
      hidden: True
      namespace: "Alignment"
      format: "{:,.1f}"
      max: 100
    APDB:
      description: "APDB metric."
      hidden: True
      namespace: "Alignment"
      format: "{:,.1f}"
    iRMSD:
      description: "iRMSD metric."
      hidden: True
      namespace: "Alignment"
      format: "{:,.1f}"
    TCS:
      description: "TCS metric."
      hidden: True
      namespace: "Alignment"
      format: "{:,.1f}"
    total_gaps:
      description: "Total amount of gaps."
      hidden: True
      namespace: "Alignment"
      format: "{:,.1f}"
    avg_gaps:
      description: "Average amount of gaps per sequence."
      hidden: True
      namespace: "Alignment"
      format: "{:,.1f}"
    NiRMSD:
      description: "NiRMSD metric."
      hidden: False
      namespace: "Alignment"
      format: "{:,.1f}"
      min: 0
    tree:
      description: "Tree used in the alignment."
      hidden: False
      namespace: "Alignment"
      scale: "Paired"
    args_tree:
      description: "Arguments used to build the tree."
      hidden: True
      namespace: "Alignment"
    args_tree_clean:
      description: "Arguments used to build the tree."
      hidden: True
      namespace: "Alignment"
    aligner:
      description: "Aligner used."
      hidden: False
      namespace: "Alignment"
      scale: "Paired"
    args_aligner:
      description: "Arguments used to run the aligner."
      hidden: True
      namespace: "Alignment"
    args_aligner_clean:
      description: "Arguments used to run the aligner."
      hidden: True
      namespace: "Alignment"

table_columns_placement:
  summary_stats:
    fasta: 90
    tree: 150
    args_tree: 170
    aligner: 200
    args_aligner: 220
    n_sequences: 250
    seqlength_mean: 280
    seqlength_median: 310
    seqlength_max: 340
    perc_sim: 370
    sp: 400
    tc: 430
    EVALUATED: 470
    APDB: 500
    iRMSD: 530
    NiRMSD: 560
    TCS: 590
    total_gaps: 620
    avg_gaps: 650

sp:
  summary_stats:
    fn: "summary_stats_eval_multiqc_table.csv"
