MULTIQC(1)

✨ MULTIQC ✨

okay bestie, this is the multiqc manual page, from the User Commands section of the manual — it's giving "output integration for RNA sequencing across tools and samples" and honestly? iconic. 💅

🌸 NAME 🌸

multiqc — output integration for RNA sequencing across tools and samples 🧬✨

🦋 SYNOPSIS 🦋

multiqc [OPTIONS] <analysis directory>

💖 DESCRIPTION 💖

okay so basically, MultiQC aggregates results from bioinformatics analyses across many samples into a single report. no cap. 🫶

It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. it's literally the group chat of bioinformatics tools — everyone's output ends up in one place. 💀

To run, supply with one or more directory to scan for analysis results. To run here, use multiqc . ✨

See http://multiqc.info for more details. 👑

Author: Phil Ewels (http://phil.ewels.co.uk) — king behaviour, honestly. 👑

✨ OPTIONS ✨

• -f, --force — Overwrite any existing reports. yes, we're bulldozing the old ones, no regrets. 🔥
• -d, --dirs — Prepend directory to sample names
• -dd, --dirs-depth INTEGER — Prepend [INT] directories to sample names. Negative number to take from start of path.
• -s, --fullnames — Do not clean the sample names (leave as full file name)
• -i, --title TEXT — Report title. Printed as page header, used for filename if not otherwise specified.
• -b, --comment TEXT — Custom comment, will be printed at the top of the report.
• -n, --filename TEXT — Report filename. Use 'stdout' to print to standard out.
• -o, --outdir TEXT — Create report in the specified output directory.
• -t, --template [default|default_dev|gathered|geo|sections|simple] — Report template to use.
• --tag TEXT — Use only modules which tagged with this keyword, eg. RNA
• --view-tags, --view_tags — View the available tags and which modules they load
• -x, --ignore TEXT — Ignore analysis files (glob expression)
• --ignore-samples TEXT — Ignore sample names (glob expression)
• --ignore-symlinks — Ignore symlinked directories and files
• --fn_as_s_name — Use the log filename as the sample name
• --replace-names PATH — Path to TSV file to rename sample names during report generation
• --sample-names PATH — Path to TSV file containing alternative sample names for renaming buttons in the report
• --sample-filters PATH — Path to TSV file containing show/hide patterns for the report
• -l, --file-list — Supply a file containing a list of file paths to be searched, one per row
• -e, --exclude [module name] — Do not use this module. Can specify multiple times.
• -m, --module [module name] — Use only this module. Can specify multiple times.
• --data-dir — Force the parsed data directory to be created.
• --no-data-dir — Prevent the parsed data directory from being created.
• -k, --data-format [tsv|json|yaml] — Output parsed data in a different format. Default: tsv
• -z, --zip-data-dir — Compress the data directory.
• -p, --export — Export plots as static images in addition to the report
• -fp, --flat — Use only flat plots (static images)
• -ip, --interactive — Use only interactive plots (HighCharts Javascript)
• --lint — Use strict linting (validation) to help code development
• --pdf — Creates PDF report with 'simple' template. Requires Pandoc to be installed.

⚠️ bestie, listen — --pdf needs Pandoc installed, so if you don't have it, this one's just gonna be sad. 😭

• --no-megaqc-upload — Don't upload generated report to MegaQC, even if MegaQC options are found
• -c, --config PATH — Specific config file to load, after those in MultiQC dir / home dir / working dir.
• --cl-config, --cl_config TEXT — Specify MultiQC config YAML on the command line
• -v, --verbose — Increase output verbosity.
• -q, --quiet — Only show log warnings
• --profile-runtime — Add analysis of how long MultiQC takes to run to the report
• --no-ansi — Disable coloured log output
• --version — Show the version and exit.
• -h, --help — Show this message and exit.

🎀 AUTHOR 🎀

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. slay. 💜

and that's the whole vibe check, bestie 🌈 — this was multiqc version 1.11, dated August 2021, straight from the MULTIQC(1) page. go forth and aggregate, you gorgeous genius. 💖✨🦋🎀🌸🫶👑