MultiQC Plugins

MultiQC plugins that you can use to extend MultiQC functionality.

MultiQC is built in such a way that externally managed Python packages can tie in to its functionality. This allows separate plugin tools to extend its capabilities, adding new modules, report templates and doing useful things with the parsed data.

The below list highlights a few such plugins - some may be useful to you if they interact with external tools which you use (eg. MultiQC_Clarity), others may be helpful as reference for writing your own plugin.

If you have written a plugin which could be featured here, please let me know! For more information about writing plugins, please see the MultiQC documentation. Also, feel free to jump onto gitter to get some help or test the water about the feasilibilty of any ideas..

Example MultiQC Plugin

A miniature example of a MultiQC plugin.

This example repository contains the following code to help you get started with writing your own MultiQC plugin.


MultiQC_Clarity is a plugin for MultiQC, able to insert project-level and sample-level metadata from the BaseSpace Clarity LIMS into MultiQC Reports.

MultiQC_Clarity connects to your Clarity LIMS installation using the API. MultiQC runs as normal, generating a list of sample names based on the contents of the files found. These sample names are passed to the MultiQC_Clarity plugin, which searches your Clarity LIMS installation for matching sample names. If exact matches are found, then the metadata configured in the config file is retrieved and entered into the report.


Plugin for multiqc tool to add in-house QC metrics about coverage, variants and general values generated by bcbio-nextgen pipeline.


MultiQC_NGI adds custom functionality for the National Genomics Infrastructure at SciLifeLab in Sweden.

Extends MultiQC with additional custom plugins and themes, allows interaction with an in-house database. Not much use for others outside of our institute directly, but can be helpful as a guide for how such plugins can be written.