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#######################################
# Example MultiQC Configuration File
#######################################
# This file can be saved either in the MultiQC installation
# directory, or as ~/.multiqc_config.yaml
# Configuration settings are taken from the following locations, in order:
# - Hardcoded in MultiQC (multiqc/utils/config.py)
# - <installation_dir>/multiqc_config.yaml
# - ~/.multiqc_config.yaml
# - Command line options
# Note that all of the values below are set to the MultiQC defaults.
# It's recommended that you delete any that you don't need.
---
# Title to use for the report.
title: null
# Prepend sample names with their directory. Useful if analysing the
# sample samples with different parameters.
prepend_dirs: False
# Default output filenames
output_fn_name: multiqc_report.html
data_dir_name: multiqc_data
# Whether to create the parsed data directory in addition to the report
make_data_dir: True
# Cleaning options for sample names. Typically, sample names are detected
# from an input filename. If any of these strings are found, they and any
# text to their right will be discarded.
# For example - file1.fq.gz_trimmed.bam_deduplicated_fastqc.zip
# would be cleaned to 'file1'
# Two options here - fn_clean_exts will remove the defaults,
# extra_fn_clean_exts will append to the defaults
extra_fn_clean_exts:
- .gz
- .fastq
- .fq
- .bam
- .sam
- .sra
- _tophat
- _star_aligned
- _fastqc
- type: remove
pattern: '.sorted'
- type: regex
pattern: '^Sample_\d+'
- type: regex_keep
pattern: '[A-Z]{3}[1-9]{4}[A,B][1-9]'
# Ignore these files / directories / paths when searching for logs
fn_ignore_files:
- .DS_Store
fn_ignore_dirs:
- annoying_dirname
fn_ignore_paths:
- '*/path/to/*_files/'
# Ignore files larger than this when searching for logs (bytes)
log_filesize_limit: 5000000
# MultiQC skips a couple of debug messages when searching files as the
# log can get very verbose otherwise. Re-enable here to help debugging.
report_readerrors: False
report_imgskips: False
# Opt-out of remotely checking that you're running the latest version
no_version_check: False
# How to plot graphs. Different templates can override these settings, but
# the default template can use interactive plots (Javascript using HighCharts)
# or flat plots (images, using MatPlotLib). With interactive plots, the report
# can prevent automatically rendering all graphs if there are lots of samples
# to prevent the browser being locked up when the report opens.
plots_force_flat: False # Try to use only flat image graphs
plots_force_interactive: False # Try to use only interactive javascript graphs
plots_flat_numseries: 100 # If neither of the above, use flat if > this number of datasets
num_datasets_plot_limit: 50 # If interactive, don't plot on load if > this number of datasets
max_table_rows: 500 # Swap tables for a beeswarm plot above this
# Overwrite module filename search patterns. See multiqc/utils/search_patterns.yaml
# for the defaults. Remove a default by setting it to null.
sp:
star:
fn: '*Log.final.out'
trimmomatic:
contents: 'Trimmomatic'
# Specify a custom logo to add to reports (uncomment to use)
custom_logo: null # '/path/to/logo.png'
custom_logo_url: null # 'https://www.example.com'
custom_logo_title: null # 'Our Institute Name'
subtitle: null # Grey text below title
intro_text: null # Set to False to remove, or your own text
# Add generic information to the top of reports
report_header_info:
- Example Config:: 'This is arbitrary'
- Another field:: 'Loaded from <code>multiqc_config_example.yaml</code>'
- Something different:: 'You can put any key-value pairs here'
- Want to know more?: 'See the <a href="http://multiqc.info/docs" target="_blank">MultiQC docs</a>'
# Overwrite the defaults of which table columns are visible by default
table_columns_visible:
FastQC:
percent_fails: False
total_sequences: True