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

It should be used in addition to the main MultiQC documentation: http://multiqc.info/docs/#coding-with-multiqc

If you have any questions, please get in touch on Gitter: https://gitter.im/ewels/MultiQC

• setup.py
  • Where the setuptools plugin hooks are defined. This is where you tell MultiQC where to find your code.
  • This file also defines how your plugin should be installed, including required python packages.
• example_plugin/
  • Installable Python packages are typically put into a directory with the same name.
• example_plugin/__init__.py
  • Python packages need an __init__.py file in every directory. Here, these are mostly empty (except the one in the my_example folder, which contains a shortcut to make the import statement shorter).
  • If you prefer, you can put all code in these files and just reference the directory name only.
• example_plugin/cli.py
  • Additional command line parameters to add to MultiQC
• example_plugin/custom_code.py
  • File to hold custom functions that can tie into the main MultiQC execution flow.
  • In this file, we define some new config defaults, including the search patterns used by the example module
• example_plugin/modules/my_example/
  • This folder contains a minimal MultiQC module which will execute along with all other MultiQC modules (as defined by the setup.py hook).

In this example plugin, I have defined a single additional command line flag - --disable-example-plugin. When specified, it sets a new MultiQC config value to True. This is checked in every plugin function; the function then returns early if it's True.

In this way, we can effectively disable the plugin code and allow native MultiQC execution. Note that a similar approach could be used to enable a custom plugin or feature.