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Ready-to-Code](https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/snakemake/snakemake)\n[![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++)\n[![Sonarcloud Status](https://sonarcloud.io/api/project_badges/measure?project=snakemake_snakemake\u0026metric=alert_status)](https://sonarcloud.io/dashboard?id=snakemake_snakemake)\n[![Conda Version](https://img.shields.io/conda/vn/bioconda/snakemake)](https://anaconda.org/bioconda/snakemake)\n[![Bioconda](https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda)](https://bioconda.github.io/recipes/snakemake/README.html)\n[![Pypi](https://img.shields.io/pypi/pyversions/snakemake.svg)](https://pypi.org/project/snakemake)\n[![docker container status](https://img.shields.io/github/actions/workflow/status/snakemake/snakemake/docker-publish.yml?color=blue\u0026label=docker%20container)](https://hub.docker.com/r/snakemake/snakemake)\n[![Stack Overflow](https://img.shields.io/badge/stack-overflow-orange.svg)](https://stackoverflow.com/questions/tagged/snakemake)\n[![Twitter](https://img.shields.io/twitter/follow/johanneskoester.svg?style=social\u0026label=Follow)](https://twitter.com/search?l=\u0026q=%23snakemake%20from%3Ajohanneskoester)\n![Mastodon Follow](https://img.shields.io/mastodon/follow/109308140471392959?domain=https%3A%2F%2Ffosstodon.org\u0026label=Follow)\n[![Discord](https://img.shields.io/discord/753690260830945390?label=discord%20chat)](https://discord.gg/NUdMtmr)\n[![Github stars](https://img.shields.io/github/stars/snakemake/snakemake?style=social)](https://github.com/snakemake/snakemake/stargazers)\n[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md) \n\n# Snakemake\n\nThe Snakemake workflow management system is a tool to create **reproducible and scalable** data analyses.\nSnakemake is highly popular, with on average more than 7 new citations per week in 2021, and almost 400k downloads.\nWorkflows are described via a human readable, Python based language.\nThey can be seamlessly scaled to server, cluster, grid and cloud environments without the need to modify the workflow definition.\nFinally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.\n\n**Homepage: https://snakemake.github.io**\n\nCopyright (c) 2012-2022 Johannes Köster \u003cjohannes.koester@uni-due.com\u003e (see 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