Scaffold Snakemake Plugins

Snakedeploy can be used to scaffold the code needed to write Snakemake plugins. It utilizes pixi for this purpose, hence you need to have it installed first. Assuming you want to create a new Snakemake executor plugin with the name something. First, create a corresponding pixi project with

$ pixi init --format pyproject snakemake-executor-plugin-something

thereby following the mandatory naming convention for Snakemake plugins, i.e. snakemake-<plugin_type>-plugin-<name>. Enter the created directory with

$ cd snakemake-executor-plugin-something

Then, you can scaffold the plugin code with Snakedeploy via

$ snakedeploy scaffold-snakemake-plugin executor

instead of executor, any of the following is possible:

• executor - to scaffold a Snakemake executor plugin,

• storage - to scaffold a Snakemake storage plugin,

• report - to scaffold a Snakemake report plugin,

• scheduler - to scaffold a Snakemake scheduler plugin.

Snakedeploy will create a pixi project with state-of-the-art skeleton code for the requested plugin type, including all required class implementations, test cases and even github actions for continous testing.

For details and additional options, run

$ snakedeploy scaffold-snakemake-plugin --help