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.