Snakemake logger plugin: sumerrs

Warning

No repository URL found in Pypi metadata. The plugin should specify a repository URL in its pyproject.toml (key 'repository'). It is unclear whether the plugin is maintained and reviewed by the official Snakemake organization (https://github.com/snakemake).

Installation

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

pip install snakemake-logger-plugin-sumerrs

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-sumerrs = "*"

Usage

In order to use the plugin, run Snakemake (>=9.11) with the corresponding value for the logger flag:

snakemake --logger sumerrs ...

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):

Settings

CLI argument	Description	Default	Choices	Required	Type
--logger-sumerrs-disable VALUE	disable collecting and printing of warnings/errors/job_fail when snakemake workflow ends. comma-separated; errors are disabled by default (job failures and warnings are reported). Pass an empty string to report errors too	'error'		✗	str
--logger-sumerrs-out VALUE	output stream for printing errors and warnings when snakemake workflow ends. default (&2) is stderr, &1 for stdout, or a file path to append at the end	'&2'		✗	str