---
name: "multiqc"
section: "1"
platform: "linux"
package: "multiqc"
version: "1.21+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/multiqc"
---

# multiqc(1)

output integration for RNA sequencing across tools and samples

## 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.