snakemake-executor-plugin-cannon

Snakemake executor plugin: cannon

This is a fork of the SLURM executor plugin for Snakemake for the Cannon cluster at Harvard University. It has all the same features as the SLURM plugin, but performs automatic partition selection for the Cannon cluster based on the resources specified in a given Snakemake rule. It also offers some error checking for partition selection.

Installation

The executor can be installed from PyPI with pip:

pip install snakemake-executor-plugin-cannon

Or from bioconda with conda/mamba:

mamba install snakemake-executor-plugin-cannon

Specifying the executor

To use the executor with Snakemake, either specify it in the command line as:

snakemake -e cannon ...

Or add it to your profile:

executor: cannon

Setting up your profile

While this plugin does automatic partition selection, the user is still responsible for specifying other resources for rules in their workflow. This is usually done through a cluster profile, but this may differ based on your workflow.

See the profile setup page for more information.

An example profile can be found at tests/cannon-test-profile/config.yaml

Features

For documentation, see the Snakemake plugin catalog.