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 .'

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

Author: Phil Ewels (http://phil.ewels.co.uk)

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|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.

AUTHOR

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