Snakemake logger plugin: spectio

Warning

This plugin is not maintained and reviewed by the official Snakemake organization.

This logger connects Snakemake to Spectio, an open-source run manager for HPC and Kubernetes that launches, monitors and relaunches Nextflow and Snakemake runs on your own cluster.

Version 0.0.0 holds the name and already works on its own: it writes each Snakemake log event as one JSON line to a file, so another program can follow a run. The bridge that reports a run to a Spectio server comes with Spectio’s first release, 0.0.1. Spectio’s documentation is at https://spectio.pages.dev.

Installation

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

pip install snakemake-logger-plugin-spectio

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-spectio = "*"

Usage

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

snakemake --logger spectio ...

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-spectio-file VALUE	File the JSON lines are appended to.	'spectio-events.jsonl'		✗