snakemake/snakemake

Health v2 · maintenance only

Adoption not part of the score

2853 stars · 654 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

Snakemake is a Python-based workflow management system for creating reproducible and scalable data analyses. Workflows are defined via a readable rule-based language and can scale from laptops to clusters, grids, and clouds with automatic software deployment via Conda and containers.

Use cases

• build reproducible data analysis pipelines
• run bioinformatics workflows on a cluster
• scale a pipeline from laptop to cloud without changing code
• manage multi-step ETL workflows with dependencies
• automatically deploy software dependencies for each workflow step
• create reusable workflow modules and wrappers
• orchestrate genomics analysis pipelines

When to choose

• you need reproducible, scalable scientific or data analysis pipelines
• you want Python-based workflow syntax with shell, script, and notebook integration
• you need to run the same workflow on a laptop, HPC cluster, or cloud
• you want automatic deployment of per-step software environments via Conda or containers

When to avoid

• you need a simple one-off script with no multi-step dependencies
• your team prefers YAML-only pipeline definitions without Python
• you need real-time streaming data processing rather than batch workflows
• you want a fully declarative DAG tool with no programming

Facets

framework · maturity stable

workflow-automation etl deployment cli data-science bioinformatics developer-tools python cli cloud cross-platform reproducibility scientific-workflows pipeline-management bioinformatics conda-integration containerization job-scheduling data-engineering automation linux macos docker

Member repositories

For agents

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