#################################################################
# MultiQC Defaults
#################################################################
# This file contains the default configuration options
# for MultiQC. IT SHOULD NOT BE EDITED. If you want to
# change any of these config options, create a new file
# in any of the following locations:
#  1. <installation_dir>/multiqc_config.yaml (not pip or conda)
#  2. ~/.multiqc_config.yaml
#  3. <working directory>/multiqc_config.yaml
#################################################################

title: null
subtitle: null
intro_text: null
report_comment: null
report_header_info: null
show_analysis_paths: True
show_analysis_time: True
config_file: null
custom_logo: null
custom_logo_url: null
custom_logo_title: null
custom_css_files: []
simple_output: false
template: "default"
profile_runtime: false
pandoc_template: null
read_count_multiplier: 0.000001
read_count_prefix: "M"
read_count_desc: "millions"
long_read_count_multiplier: 0.001
long_read_count_prefix: "K"
long_read_count_desc: "thousands"
base_count_multiplier: 0.000001
base_count_prefix: "Mb"
base_count_desc: "millions"
output_fn_name: "multiqc_report.html"
data_dir_name: "multiqc_data"
plots_dir_name: "multiqc_plots"
data_format: "tsv"
module_tag: []
force: false
no_ansi: false
quiet: false
prepend_dirs: false
prepend_dirs_depth: 0
prepend_dirs_sep: " | "
file_list: false

make_data_dir: true
zip_data_dir: false
data_dump_file: true
megaqc_url: false
megaqc_access_token: null
megaqc_timeout: 30
export_plots: false
make_report: true
plots_force_flat: false
plots_force_interactive: false
plots_flat_numseries: 100
num_datasets_plot_limit: 50
collapse_tables: true
max_table_rows: 500
table_columns_visible: {}
table_columns_placement: {}
table_columns_name: {}
table_cond_formatting_colours:
  - blue: "#337ab7"
  - lbue: "#5bc0de"
  - pass: "#5cb85c"
  - warn: "#f0ad4e"
  - fail: "#d9534f"
table_cond_formatting_rules:
  all_columns:
    pass:
      - s_eq: "pass"
      - s_eq: "true"
    warn:
      - s_eq: "warn"
      - s_eq: "unknown"
    fail:
      - s_eq: "fail"
      - s_eq: "false"
  # PURPLE module - QC Status column
  # TODO: Should update the table plotting code so that this can go in pconfig
  QCStatus:
    fail:
      - s_contains: "fail"
decimalPoint_format: null
thousandsSep_format: null
remove_sections: []
section_comments: {}
lint: False
custom_plot_config: {}
custom_table_header_config: {}

ignore_symlinks: false
ignore_images: true
fn_ignore_dirs:
  - "multiqc_data"
  - ".git"
  - "icarus_viewers" # quast
  - "runs_per_reference" # quast
  - "not_aligned" # quast
  - "contigs_reports" # quast

fn_ignore_paths:
  - "*/work/??/??????????????????????????????" # Nextflow work directories - always same hash lengths
  - "*/.snakemake"
  - "*/.singularity" # Singularity cache path
  - "*/__pycache__"
  - "*/site-packages/multiqc" # MultiQC installation directory
sample_names_ignore: []
sample_names_ignore_re: []
sample_names_rename_buttons: []
sample_names_replace: {}
sample_names_replace_regex: False
sample_names_replace_exact: False
sample_names_replace_complete: False
sample_names_rename: []
show_hide_buttons: []
show_hide_patterns: []
show_hide_regex: []
show_hide_mode: []
no_version_check: false
log_filesize_limit: 10000000
report_readerrors: false
skip_generalstats: false
data_format_extensions:
  tsv: "txt"
  json: "json"
  yaml: "yaml"
export_plot_formats:
  - "png"
  - "svg"
  - "pdf"

# Custom Config settings
custom_content:
  order: []

# Option to disable sample name cleaning if desired
fn_clean_sample_names: true

# Option to use the filename as the sample name if desired
# Set to True to apply for all modules. Define a list of search pattern keys to be specific.
use_filename_as_sample_name: false

# Used for cleaning sample names. Should be strings.
# NB: These are removed in order!
fn_clean_exts:
  - ".gz"
  - ".fastq"
  - ".fq"
  - ".bam"
  - ".sam"
  - ".sra"
  - ".vcf"
  - ".dat"
  - "_tophat"
  - ".pbmarkdup.log"
  - ".log"
  - ".stderr"
  - ".out"
  - ".spp"
  - ".fa"
  - ".fasta"
  - ".png"
  - ".jpg"
  - ".jpeg"
  - ".html"
  - "Log.final"
  - "ReadsPerGene"
  - ".flagstat"
  - "_star_aligned"
  - "_fastqc"
  - ".hicup"
  - ".counts"
  - "_counts"
  - ".txt"
  - ".tsv"
  - ".csv"
  - ".aligned"
  - "Aligned"
  - ".merge"
  - ".deduplicated"
  - ".dedup"
  - ".clean"
  - ".sorted"
  - ".report"
  - "| stdin"
  - ".geneBodyCoverage"
  - ".inner_distance_freq"
  - ".junctionSaturation_plot.r"
  - ".pos.DupRate.xls"
  - ".GC.xls"
  - "_slamdunk"
  - "_bismark"
  - ".conpair"
  - ".concordance"
  - ".contamination"
  - ".BEST.results"
  - "_peaks.xls"
  - ".relatedness"
  - ".cnt"
  - ".aqhist"
  - ".bhist"
  - ".bincov"
  - ".bqhist"
  - ".covhist"
  - ".covstats"
  - ".ehist"
  - ".gchist"
  - ".idhist"
  - ".ihist"
  - ".indelhist"
  - ".lhist"
  - ".mhist"
  - ".qahist"
  - ".qchist"
  - ".qhist"
  - ".rpkm"
  - ".selfSM"
  - ".extendedFrags"
  - "_SummaryStatistics"
  - ".purple.purity"
  - ".purple.qc"
  - ".trim"
  - ".bowtie2"
  - ".mkD"
  - ".highfreq"
  - ".lowfreq"
  - ".consensus"
  - ".snpEff"
  - ".snpeff"
  - ".scaffolds"
  - ".contigs"
  - ".kraken2"
  - ".ccurve"
  - ".hisat2"
  - "_duprate"
  - ".markdup"
  - ".read_distribution"
  - ".junction_annotation"
  - ".infer_experiment"
  - ".biotype"
  - ".ivar"
  - ".mpileup"
  - ".primer_trim"
  - ".mapped"
  - ".vep"
  - "_vep"
  - "ccs"
  - "_NanoStats"
  - ".cutadapt"
  - ".mosdepth"
  - _gopeaks

# These are removed after the above, only if sample names
# start or end with this string. Again, removed in order.
fn_clean_trim:
  - "."
  - ":"
  - "_"
  - "-"
  - ".r"
  - "_val"
  - ".idxstats"
  - "_trimmed"
  - ".trimmed"
  - ".csv"
  - ".yaml"
  - ".yml"
  - ".json"
  - "_mqc"
  - "short_summary_"
  - "_summary"
  - ".summary"
  - ".align"
  - ".h5"
  - "_matrix"
  - ".stats"
  - ".hist"
  - ".phased"

# Files to ignore when indexing files.
# Grep file match patterns.
fn_ignore_files:
  - ".DS_Store"
  - ".py[cod]"
  - "*.bam"
  - "*.bai"
  - "*.sam"
  - "*.fq.gz"
  - "*.fastq.gz"
  - "*.fq"
  - "*.fastq"
  - "*.fa"
  - "*.gtf"
  - "*.bed"
  - "*.vcf"
  - "*.tbi"
  - "*.txt.gz"
  - "*.pdf"
  - "*.md5"
  - "*[!s][!u][!m][!_\\.m][!mva][!qer][!cpy].html" # Allow _mqc.html, _vep.html and summary.html files
  - multiqc_data.json

# Favourite modules that should appear at the top in preference
# This is in addition to those below. These appear above _all_ other
# modules (even those not present in the below list).
top_modules: []

# Order that modules should appear in report. Try to list in order of analysis.
module_order:
  # MultiQC general module for catching output from custom scripts
  - "custom_content"
  # Post-alignment QC
  - ccs:
      module_tag:
        - DNA
        - RNA
        - PacBio
  - ngsderive:
      module_tag:
        - DNA
        - RNA
  - purple:
      module_tag:
        - DNA
        - cancer
  - conpair:
      module_tag:
        - WGS
        - cancer
        - DNA
  - lima:
      module_tag:
        - RNA
        - DNA
        - PacBio
  - peddy:
      module_tag:
        - DNA
  - somalier:
      module_tag:
        - DNA
        - Methylation
        - WGS
        - cancer
        - chip
        - RNA
  - methylQA:
      module_tag:
        - Methylation
        - DNA
  - mosdepth:
      module_tag:
        - DNA
        - RNA
  - phantompeakqualtools:
      module_tag:
        - chip
  - qualimap:
      module_tag:
        - DNA
        - RNA
  - preseq:
      module_tag:
        - DNA
        - RNA
  - hifiasm:
      module_tag:
        - DNA
        - Denovo
        - PacBio
  - quast:
      module_tag:
        - DNA
        - metagenomics
        - Denovo
  - qorts:
      module_tag:
        - RNA
  - rna_seqc:
      module_tag:
        - RNA
  - rockhopper:
      module_tag:
        - RNA
  - rsem:
      module_tag:
        - RNA
  - rseqc:
      module_tag:
        - RNA
  - busco:
      module_tag:
        - Denovo
  - bustools:
      module_tag:
        - RNA
  - goleft_indexcov:
      module_tag:
        - DNA
  - gffcompare:
      module_tag:
        - RNA
  - disambiguate:
      module_tag:
        - RNA
  - supernova:
      module_tag:
        - DNA
        - Denovo
  - deeptools:
      module_tag:
        - DNA
        - RNA
        - chip
  - sargasso:
      module_tag:
        - RNA
  - verifybamid:
      module_tag:
        - DNA
  - mirtrace:
      module_tag:
        - smRNA
        - miRNA
  - happy:
      module_tag:
        - DNA
  - mirtop:
      module_tag:
        - miRNA
  - sambamba:
      module_tag:
        - DNA

  # Post-alignment processing
  - gopeaks:
      module_tag:
        - DNA
        - CUT&TAG
        - CUT&RUN
  - homer:
      module_tag:
        - RNA
        - DNA
        - chip
  - hops:
      module_tag:
        - DNA
        - metagenomics
        - ancient
  - macs2:
      module_tag:
        - chip
  - theta2:
      module_tag:
        - DNA
        - cancer
  - snpeff:
      module_tag:
        - DNA
  - gatk:
      module_tag:
        - DNA
  - htseq:
      module_tag:
        - DNA
        - RNA
  - bcftools:
      module_tag:
        - DNA
  - featureCounts:
      module_tag:
        - DNA
        - RNA
  - fgbio:
      module_tag:
        - DNA
        - RNA
        - umi
  - dragen:
      module_tag:
        - DNA
        - RNA
  - dragen_fastqc:
      module_tag:
        - DNA
        - RNA
  - dedup:
      module_tag:
        - DNA
        - ancient
  - pbmarkdup:
      module_tag:
        - DNA
        - RNA
  - damageprofiler:
      module_tag:
        - DNA
        - ancient
  - biobambam2:
      module_tag:
        - DNA
        - RNA
  - jcvi:
      module_tag:
        - denovo
  - mtnucratio:
      module_tag:
        - DNA
        - ancient
  - picard:
      module_tag:
        - DNA
        - RNA
  - vep:
      module_tag:
        - DNA
  - sentieon:
      module_tag:
        - DNA
  - prokka:
      module_tag:
        - prokarytotic
        - denovo
  - qc3C:
      module_tag:
        - hi-c
  - nanostat:
      module_tag:
        - DNA
        - RNA
        - Methylation
        - WGS
  - samblaster:
      module_tag:
        - DNA
        - RNA
  - samtools:
      module_tag:
        - DNA
        - RNA
  - sexdeterrmine:
      module_tag:
        - DNA
  - eigenstratdatabasetools:
      module_tag:
        - DNA
  - bamtools:
      module_tag:
        - DNA
        - RNA
  - jellyfish:
      module_tag:
        - DNA
  - vcftools:
      module_tag:
        - DNA
  - longranger:
      module_tag:
        - DNA
        - WGS
  - stacks:
      module_tag:
        - DNA
  - varscan2:
      module_tag:
        - DNA
  - snippy:
      module_tag:
        - DNA
        - prokarytotic
  - umitools:
      module_tag:
        - DNA
        - RNA

  # Alignment tool stats
  - bbmap:
      module_tag:
        - DNA
        - RNA
  - bismark:
      module_tag:
        - DNA
        - methylation
  - biscuit:
      module_tag:
        - DNA
        - methylation
  - diamond:
      module_tag:
        - Protein
        - DNA
  - hicexplorer:
      module_tag:
        - hi-c
  - hicup:
      module_tag:
        - hi-c
  - hicpro:
      module_tag:
        - hi-c
  - salmon:
      module_tag:
        - RNA
  - kallisto:
      module_tag:
        - RNA
  - slamdunk:
      module_tag:
        - slam
  - star:
      module_tag:
        - RNA
  - hisat2:
      module_tag:
        - RNA
  - tophat:
      module_tag:
        - RNA
  - bowtie2:
      module_tag:
        - RNA
  - bowtie1:
      module_tag:
        - RNA
  - cellranger:
      module_tag:
        - RNA
        - single-cell
  - snpsplit:
      module_tag:
        - DNA
        - RNA
        - methylation
        - allele-specific
  - odgi:
      module_tag:
        - DNA
        - pangenome
  - pangolin:
      module_tag:
        - DNA
        - virus
  - nextclade:
      module_tag:
        - RNA
        - virus
  # Pre-alignment QC
  - humid:
      module_tag:
        - DNA
        - RNA
        - umi
  - kat:
      module_tag:
        - DNA
  - leehom:
      module_tag:
        - RNA
        - DNA
  - adapterRemoval:
      module_tag:
        - RNA
        - DNA
  - bbduk:
      module_tag:
        - RNA
        - DNA
  - clipandmerge:
      module_tag:
        - DNA
        - ancient
  - cutadapt:
      module_tag:
        - RNA
        - DNA
  - flexbar:
      module_tag:
        - RNA
        - DNA
  - kaiju:
      module_tag:
        - DNA
        - metagenomics
  - kraken:
      module_tag:
        - DNA
        - metagenomics
  - malt:
      module_tag:
        - DNA
        - metagenomics
        - ancient
  - motus:
      module_tag:
        - RNA
        - DNA
  - trimmomatic:
      module_tag:
        - RNA
        - DNA
  - sickle:
      module_tag:
        - RNA
        - DNA
  - skewer:
      module_tag:
        - RNA
        - DNA
  - sortmerna:
      module_tag:
        - RNA
        - DNA
  - biobloomtools:
      module_tag:
        - RNA
        - DNA
  - fastq_screen:
      module_tag:
        - RNA
        - DNA
  - afterqc:
      module_tag:
        - RNA
        - DNA
  - fastp:
      module_tag:
        - RNA
        - DNA
  - fastqc:
      module_tag:
        - RNA
        - DNA
  - filtlong:
      module_tag:
        - DNA
        - ONT
        - PacBio
  - prinseqplusplus:
      module_tag:
        - RNA
        - DNA
  - pychopper:
      module_tag:
        - RNA
  - porechop:
      module_tag:
        - DNA
        - nanopore
  - pycoqc:
      module_tag:
        - DNA
        - RNA
  - minionqc:
      module_tag:
        - DNA
        - RNA
  - anglerfish:
      module_tag:
        - DNA
        - Illumina
        - ONT
  - multivcfanalyzer:
      module_tag:
        - DNA
        - ancient
  - clusterflow:
      module_tag:
        - RNA
        - DNA
        - methylation
  - checkqc:
      module_tag:
        - DNA
        - RNA
        - Illumina
  - bcl2fastq:
      module_tag:
        - RNA
        - DNA
        - methylation
  - bclconvert:
      module_tag:
        - RNA
        - DNA
        - methylation
  - interop:
      module_tag:
        - RNA
        - DNA
        - methylation
  - ivar:
      module_tag:
        - RNA
        - epidemiology
        - virus
  - flash:
      module_tag:
        - DNA
        - RNA
  - seqyclean:
      module_tag:
        - DNA
        - RNA
  - optitype:
      module_tag:
        - DNA
        - RNA
        - HLATyping
  - whatshap:
      module_tag:
        - DNA
