Snakemake logger plugin: github-status
A Snakemake logger plugin that reports to the Github commit status. The plugin assumes that it is used in combination with working directories that are controlled by git and associated to a Github repository. It then reports logging events to the Github status API, such that Github displays the status of workflow runs attached to the current commit. Github’s status markers (running, success, failed) are thereby used to represent the state of the workflow execution, while the status messages are used to report on the number of completed and failed jobs.
Installation
Install this plugin by installing it with pip or mamba directly, e.g.:
pip install snakemake-logger-plugin-github-status
Or, if you are using pixi, add the plugin to your pixi.toml. Be careful to put it under the right dependency type based on the plugin’s availability, e.g.:
snakemake-logger-plugin-github-status = "*"
Usage
In order to use the plugin, run Snakemake (>=9.11) with the corresponding value for the logger flag:
snakemake --logger github-status ...
with ... being any additional arguments you want to use.
Settings
The logger plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):