| MULTIQC(1) | User Commands | MULTIQC(1) |
NAME¶
multiqc - output integration for RNA sequencing across tools and samples
SYNOPSIS¶
multiqc [OPTIONS] <analysis directory>
DESCRIPTION¶
MultiQC aggregates results from bioinformatics analyses across many samples into a single report.
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.
To run, supply with one or more directory to scan for analysis results. To run here, use 'multiqc .'
OPTIONS¶
- -f, --force
- Overwrite any existing reports
- -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|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
- --sample-names PATH
- File containing alternative sample names
- -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
- Creates PDF report with 'simple' template. Requires Pandoc to be installed.
- --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
- --version
- Show the version and exit.
- -h, --help
- Show this message and exit.
SEE ALSO¶
See http://multiqc.info for more details.
AUTHOR¶
Phil Ewels (http://phil.ewels.co.uk)
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
| July 2019 | multiqc 1.7 |