multiqc - output integration for RNA sequencing across tools and
samples
multiqc [OPTIONS] <analysis
directory>
- 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 .'
- See http://multiqc.info for more details.
- Author: Phil Ewels (http://phil.ewels.co.uk)
- -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|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.
- --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.
This manpage was written by Nilesh Patra for the Debian
distribution and can be used for any other usage of the program.