snakemake-logger-plugin-prometheus 0.1.1

Snakemake logger plugin that exposes job info to prometheus.

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

Metric Name	Type	Labels	Description
snakemake_jobs_submitted	Gauge	rule	Jobs known to the scheduler (Queued + Running). Increments when a job is ready, decrements when finished.
snakemake_jobs_running	Gauge	rule	Jobs actively executing. Increments when execution starts, decrements when finished.
snakemake_jobs_finished_total	Counter	status (finished/failed), rule	Cumulative count of completed jobs. Useful for throughput rates.
snakemake_jobs_planned_total	Gauge	rule	Total jobs planned for the workflow. Updates dynamically if checkpoints trigger DAG re-evaluation.

Resources

Metric Name	Type	Labels	Description
snakemake_resource_usage_total	Gauge	resource	Total resources currently consumed by Running jobs (e.g., threads, mem_mb).
snakemake_resource_limits	Gauge	resource	Maximum resources available to the workflow (CLI limits or cluster capacity).

Workflow Status

Metric Name	Type	Labels	Description
snakemake_workflow_progress	Gauge	type (done/total)	High-level progress counters.
snakemake_errors_total	Counter	None	Total number of workflow-level errors.

Grafana Query Examples

Here are common queries to visualize this data:

Description	Query
Queued Jobs	sum(snakemake_jobs_submitted) - sum(snakemake_jobs_running)
Running Jobs	sum(snakemake_jobs_running)
Throughput (Jobs/Minute)	sum(rate(snakemake_jobs_finished_total{status="finished"}[5m])) * 60
Resource Utilization %	sum(snakemake_resource_usage_total{resource="threads"}) / sum(snakemake_resource_limits{resource="threads"}) * 100
Failure Rate	sum(rate(snakemake_jobs_finished_total{status="failed"}[5m]))

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