Snakemake executor plugin: cluster-generic

Warning

No documentation found in repository https://github.com/snakemake/snakemake-executor-plugin-cluster-generic. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instractions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-executor-plugin-cluster-generic

Usage

In order to use the plugin, run Snakemake (>=8.0) with the corresponding value for the executor flag:

snakemake --executor cluster-generic ...

with ... being any additional arguments you want to use.

The executor plugin has the following settings:

Settings

CLI argument	Description	Default	Choices	Required	Type
--cluster-generic-submit-cmd VALUE	Command for submitting jobs	None		✓
--cluster-generic-status-cmd VALUE	Command for retrieving job status	None		✗
--cluster-generic-cancel-cmd VALUE	Command for cancelling jobs. Expected to take one or more jobids as arguments.	None		✗
--cluster-generic-cancel-nargs VALUE	Number of jobids to pass to cancel_cmd. If more are given, cancel_cmd will be called multiple times.	20		✗
--cluster-generic-sidecar-cmd VALUE	Command for sidecar process.	None		✗