multiqc_config_overall.yaml

# Top of the page info
title: "Overall Run MultiQC Report"
subtitle: "Run QC statistics and plots"
report_comment: >
  This report contains viral sequencing metrics for all samples ran in the pipeline.
  Individual sample reports are also available to provide more detailed information on each sample

# Other things
data_format: "yaml"
max_table_rows: 10000
show_analysis_paths: false
disable_version_detection: true

# General Statistics Table
skip_generalstats: true

# Modules/tools supported that we only want to grab
run_modules:
  - custom_content
  - samtools
  - qualimap
  - bcftools
  - nanostat
  - snpeff

# Order for reports
module_order:
  - nanostat:
    name: Nanostat filtered fastq statistics
    path_filters:
      - "*.nanostat.txt"
  - samtools
  - qualimap
  - bcftools
  - snpeff

report_section_order:
  software_versions:
    order: -1000

# Custom data here
custom_data:
  # QC CSV
  qc_csv_table:
    section_name: "Overall Metrics Table"
    description: >
      This table shows the overall quality control metrics for all samples in the run
    plot_type: "table"
    pconfig:
      id: "qc_csv_table"
      table_title: "Overall QC Table"
      namespace: "Overall QC Table"
      col1_header: "Sample"
      only_defined_headers: True
      format: "{:,.0f}"
    headers:
      sample:
        scale: False
      qc_pass:
        title: "QC Pass"
        description: "Overall status of the sample"
        cond_formatting_rules:
          warn: [{"s_ne": "PASS"}]
      run_status:
        title: "Run Status"
        description: "Overall status of the run taking negative control samples into account"
        cond_formatting_rules:
          warn: [{"s_ne": "PASS"}]
      num_aligned_reads:
        title: "# Aligned Reads"
        description: "Number of aligned reads used for variant calling and consensus generation"
        hidden: False
      genome_completeness:
        title: "Genome Completeness"
        description: "Float value for how many bases in the genome were called with 1.0 being 100%"
        scale: "RdYlGn"
        min: 0
        max: 1
        format: "{:,.4f}"
      median_sequencing_depth:
        title: "Median Depth"
        description: "Median sequencing depth of the sample"
      total_variants:
        title: "Total Variants"
        description: "Total number of variant sites in the sample"
        scale: "Greens"
      num_snps:
        title: "# SNPs"
        description: "Number of individual SNPs in the sample"
        min: 0
        scale: "PuBu"
      num_deletions:
        title: "# Deletions"
        description: "The total number of deleted bases in the sample"
        min: 0
        scale: "Purples"
      num_deletion_sites:
        title: "# Deletion Sites"
        description: "The number of sites in the genome containing a deletion"
        min: 0
        scale: "Purples"
      num_insertions:
        title: "# Insertions"
        description: "The total number of inserted bases in the sample"
        min: 0
        scale: "Oranges"
      num_insertion_sites:
        title: "# Insertion Sites"
        description: "The number of sites in the genome containing an insertion"
        min: 0
        scale: "Oranges"
      possible_frameshift_variants:
        title: "Possible Frameshift Variants"
        description: "Variants detected by SnpEFF as containing a frameshift or if SnpEFF was not run, indels that fail a divisible by 3 check"
        # Note that the order here must be kept or the no_data will be yellow
        cond_formatting_rules:
          pass: [{"s_eq": "none"}]
          frameshift: [{"s_ne": "none"}]
          no_data: [{"s_eq": "NA"}]
        cond_formatting_colours:
          - 1:
            frameshift: "#f0ad4e" # Yellow Warn colour
          - 2:
            no_data: "#000000" # Black
      neg_control_info:
        title: "Neg Control Status"
        description: "If the sample is a negative control gives its status as PASS/WARN"

  # Amplicons section
  amplicon_depth:
    parent_id: amplicons_qc
    parent_name: "Amplicon Summary"
    parent_description: >
      Custom amplicon plots to show how deep each amplicon is sequenced and how complete each amplicon is
    id: 'amplicon_depth'
    file_format: 'tsv'
    section_name: 'Amplicon Depth Lineplot'
    description: >
      Calculated from the primertrimmed sorted bam file using bedtools coverage
      looking for reads that overlap 85% of the given amplicon region
    plot_type: 'linegraph'
    pconfig:
      id: 'amplicon_depth'
      title: 'Amplicon Depth'
      xlab: 'Amplicon ID'
      ylab: 'Read Depth'
      logswitch: True
      logswitch_active: False
      categories: True
      ymin: 0
  amplicon_completeness:
    parent_id: amplicons_qc
    file_format: 'csv'
    section_name: 'Amplicon Completeness'
    description: >
      Heatmap showing how complete each amplicon is based on the consensus sequence.
      Amplicon completeness is calculated using the number of Ns in the amplicon compared to the amplicon length.
      A 1.0 means the amplicon is fully sequenced while a 0 means that there were no bases called in the amplicon.
      Note that as amplicons overlap, a fully dropped amplicon could still have some completeness from its two neighbours
    id: 'amplicon_completeness'
    plot_type: 'heatmap'
    pconfig:
      id: 'amplicon_completeness'
      title: 'Amplicon Completeness'
      xTitle: 'Amplicon ID'
      xcats_samples: False
      ycats_samples: True
      square: False
      min: 0
      max: 1
      colstops: [
        [0, '#a50026'],
        [0.1, '#d73027'],
        [0.2, '#f46d43'],
        [0.3, '#fdae61'],
        [0.4, '#fee08b'],
        [0.5, '#ffffbf'],
        [0.6, '#d9ef8b'],
        [0.7, '#a6d96a'],
        [0.8, '#66bd63'],
        [0.9, '#1a9850'],
        [1, '#006837'],
      ]

# Extensions to clean from names
extra_fn_clean_exts:
  - '.nanostat'
  - '.ann'

# Search Pathes
sp:
  qc_csv_table:
    fn: '*.qc.csv'
  amplicon_depth:
    fn: '*_ampdepth.tsv'
  amplicon_completeness:
    fn: "merged_amplicon_completeness.csv"