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 instructions 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.

Settings

The executor plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):

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		✗