Snakemake Prometheus Logger Plugin

A Snakemake logger plugin that exposes workflow metrics via a Prometheus-compatible HTTP endpoint.

Installation

You can install this plugin via pip:

pip install snakemake-logger-plugin-prometheus

Or via Pixi/Conda if available in your channels.

Usage

To use this logger, run Snakemake with the --logger prometheus flag.

snakemake --logger prometheus ...

Pull Mode (Default)

By default, the metrics server runs on port 8000. Prometheus scrapes this address. You can change the port using the --logger-prometheus-port flag:

snakemake --logger prometheus --logger-prometheus-port 9090 ...

Push Mode (Pushgateway)

If you cannot expose a port or prefer pushing metrics, specify a Pushgateway URL. The plugin will push metrics every 15 seconds.

snakemake --logger prometheus --logger-prometheus-push-gateway http://localhost:9091

You can optionally set the job name used in the Pushgateway (default: "snakemake"):

snakemake --logger prometheus --logger-prometheus-push-gateway http://localhost:9091 --logger-prometheus-push-job-name my-workflow

Available Metrics

Job Lifecycle

Resources

Workflow Status

Grafana Query Examples

Here are common queries to visualize this data:

Development

This project uses pixi for dependency management and uv for building/publishing.

• Install dependencies: pixi install
• Run tests: pixi run test
• Run code formatting and linting: pixi run qc
• Build package: pixi run build
• Publish package: pixi run publish