https://github.com/snakemake/snakemake

This is the development home of the workflow management system Snakemake. For general information, see
https://github.com/snakemake/snakemake

reproducibility snakemake workflow-management

Last synced: 28 days ago
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This is the development home of the workflow management system Snakemake. For general information, see

• Host: GitHub
• URL: https://github.com/snakemake/snakemake
• Owner: snakemake
• License: mit
• Created: 2019-10-04T14:58:11.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2024-10-29T09:13:41.000Z (6 months ago)
• Last Synced: 2024-10-29T09:26:44.996Z (6 months ago)
• Topics: reproducibility, snakemake, workflow-management
• Language: HTML
• Homepage: https://snakemake.github.io
• Size: 88.6 MB
• Stars: 2,266
• Watchers: 19
• Forks: 552
• Open Issues: 1,141
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.md
  • Code of conduct: CODE_OF_CONDUCT.md
  • Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

• awesome-institutional-hpc - Snakemake - File based processing pipeline framework with workflows written on Python but additional support for CLI programs, Julia and R with SLURM support through either: (Workflow managers and distributed computing frameworks)
• awesome-production-machine-learning - Snakemake - Workflow management system for reproducible and scalable data analyses. (Data Pipeline)
• awesome-python-machine-learning-resources - GitHub - 59% open · ⏱️ 25.08.2022): (工作流程和实验跟踪)
• StarryDivineSky - snakemake/snakemake

README

        
[![Gitpod Ready-to-Code](https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/snakemake/snakemake)

[![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/snakemake/snakemake/main.yml?label=tests)](https://github.com/snakemake/snakemake/actions?query=branch%3Amain++)

[![Sonarcloud Status](https://sonarcloud.io/api/project_badges/measure?project=snakemake_snakemake&metric=alert_status)](https://sonarcloud.io/dashboard?id=snakemake_snakemake)

[![Conda Version](https://img.shields.io/conda/vn/bioconda/snakemake)](https://anaconda.org/bioconda/snakemake)

[![Bioconda](https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda)](https://bioconda.github.io/recipes/snakemake/README.html)

[![Pypi](https://img.shields.io/pypi/pyversions/snakemake.svg)](https://pypi.org/project/snakemake)

[![docker container status](https://img.shields.io/github/actions/workflow/status/snakemake/snakemake/docker-publish.yml?color=blue&label=docker%20container)](https://hub.docker.com/r/snakemake/snakemake)

[![Stack Overflow](https://img.shields.io/badge/stack-overflow-orange.svg)](https://stackoverflow.com/questions/tagged/snakemake)

[![Twitter](https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow)](https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester)

![Mastodon Follow](https://img.shields.io/mastodon/follow/109308140471392959?domain=https%3A%2F%2Ffosstodon.org&label=Follow)

[![Discord](https://img.shields.io/discord/753690260830945390?label=discord%20chat)](https://discord.gg/NUdMtmr)

[![Github stars](https://img.shields.io/github/stars/snakemake/snakemake?style=social)](https://github.com/snakemake/snakemake/stargazers)

[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md) 

# Snakemake

The Snakemake workflow management system is a tool to create **reproducible and scalable** data analyses.

Snakemake is highly popular, with on average more than 7 new citations per week in 2021, and almost 400k downloads.

Workflows are described via a human readable, Python based language.

They can be seamlessly scaled to server, cluster, grid and cloud environments without the need to modify the workflow definition.

Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

**Homepage: https://snakemake.github.io**

Copyright (c) 2012-2022 Johannes Köster  (see LICENSE)