.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH MULTIQC "1" "July 2019" "multiqc 1.7" "User Commands"
.SH NAME
multiqc \- output integration for RNA sequencing across tools and samples
.SH SYNOPSIS
.B multiqc
[\fI\,OPTIONS\/\fR] \fI\,<analysis directory>\/\fR
.SH DESCRIPTION
MultiQC aggregates results from bioinformatics analyses across many
samples into a single report.
.P
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.
.P
To run, supply with one or more directory to scan for analysis results. To
run here, use 'multiqc .'
.SH OPTIONS
.TP
\fB\-f\fR, \fB\-\-force\fR
Overwrite any existing reports
.TP
\fB\-d\fR, \fB\-\-dirs\fR
Prepend directory to sample names
.TP
\fB\-dd\fR, \fB\-\-dirs\-depth\fR INTEGER
Prepend [INT] directories to sample names.
Negative number to take from start of path.
.TP
\fB\-s\fR, \fB\-\-fullnames\fR
Do not clean the sample names (leave as full
file name)
.TP
\fB\-i\fR, \fB\-\-title\fR TEXT
Report title. Printed as page header, used
for filename if not otherwise specified.
.TP
\fB\-b\fR, \fB\-\-comment\fR TEXT
Custom comment, will be printed at the top
of the report.
.TP
\fB\-n\fR, \fB\-\-filename\fR TEXT
Report filename. Use 'stdout' to print to
standard out.
.TP
\fB\-o\fR, \fB\-\-outdir\fR TEXT
Create report in the specified output
directory.
.TP
\fB\-t\fR, \fB\-\-template\fR [default|default_dev|geo|sections|simple]
Report template to use.
.TP
\fB\-\-tag\fR TEXT
Use only modules which tagged with this
keyword, eg. RNA
.TP
\fB\-\-view\-tags\fR, \fB\-\-view_tags\fR
View the available tags and which modules
they load
.TP
\fB\-x\fR, \fB\-\-ignore\fR TEXT
Ignore analysis files (glob expression)
.TP
\fB\-\-ignore\-samples\fR TEXT
Ignore sample names (glob expression)
.TP
\fB\-\-ignore\-symlinks\fR
Ignore symlinked directories and files
.TP
\fB\-\-sample\-names\fR PATH
File containing alternative sample names
.TP
\fB\-l\fR, \fB\-\-file\-list\fR
Supply a file containing a list of file
paths to be searched, one per row
.TP
\fB\-e\fR, \fB\-\-exclude\fR [module name]
Do not use this module. Can specify multiple
times.
.TP
\fB\-m\fR, \fB\-\-module\fR [module name]
Use only this module. Can specify multiple
times.
.TP
\fB\-\-data\-dir\fR
Force the parsed data directory to be
created.
.TP
\fB\-\-no\-data\-dir\fR
Prevent the parsed data directory from being
created.
.TP
\fB\-k\fR, \fB\-\-data\-format\fR [tsv|json|yaml]
Output parsed data in a different format.
Default: tsv
.TP
\fB\-z\fR, \fB\-\-zip\-data\-dir\fR
Compress the data directory.
.TP
\fB\-p\fR, \fB\-\-export\fR
Export plots as static images in addition to
the report
.TP
\fB\-fp\fR, \fB\-\-flat\fR
Use only flat plots (static images)
.TP
\fB\-ip\fR, \fB\-\-interactive\fR
Use only interactive plots (HighCharts
Javascript)
.TP
\fB\-\-lint\fR
Use strict linting (validation) to help code
development
.TP
\fB\-\-pdf\fR
Creates PDF report with 'simple' template.
Requires Pandoc to be installed.
.TP
\fB\-\-no\-megaqc\-upload\fR
Don't upload generated report to MegaQC,
even if MegaQC options are found
.TP
\fB\-c\fR, \fB\-\-config\fR PATH
Specific config file to load, after those in
MultiQC dir / home dir / working dir.
.TP
\fB\-\-cl\-config\fR, \fB\-\-cl_config\fR TEXT
Specify MultiQC config YAML on the command
line
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Increase output verbosity.
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Only show log warnings
.TP
\fB\-\-version\fR
Show the version and exit.
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this message and exit.
.SH SEE ALSO
See http://multiqc.info for more details.
.SH AUTHOR
Phil Ewels (http://phil.ewels.co.uk)
.P
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.