Repositories list

• snakemake

  Public
  This is the development home of the workflow management system Snakemake. For general information, see

  snakemakereproducibilityworkflow-management

  Python

  •

  MIT License

  •605•2.6k•1.1k•97•Updated Aug 29, 2025Aug 29, 2025

• snakefmt

  Public
  The uncompromising Snakemake code formatter

  pythonformatterfmt+ 5bioinformaticscodeblackcodeformattersnakemake

  Python

  •

  MIT License

  •33•176•18•2•Updated Aug 29, 2025Aug 29, 2025

• snakemake-wrappers

  Public
  This is the development home of the Snakemake wrapper repository, see

  Python

  •196•231•16•24•Updated Aug 29, 2025Aug 29, 2025

• snakemake-plugin-catalog

  Public
  An automatically updated catalog of Snakemake plugins and their documentation

  Python

  •

  MIT License

  •4•3•3•4•Updated Aug 27, 2025Aug 27, 2025

• snakemake-workflow-catalog

  Public
  A statically generated catalog of available Snakemake workflows

  Python

  •

  MIT License

  •11•35•5•0•Updated Aug 25, 2025Aug 25, 2025

• snakemake.github.io

  Public
  Snakemake homepage

  snakemakehomepage

  HTML

  •

  MIT License

  •3•3•0•0•Updated Aug 25, 2025Aug 25, 2025

• snakemake-executor-plugin-slurm

  Public
  A Snakemake executor plugin for submitting jobs to a SLURM cluster

  Python

  •

  MIT License

  •37•37•36•7•Updated Aug 21, 2025Aug 21, 2025

• snakemake-interface-software-deployment-plugins

  Public
  A stable interface for Snakemake software deployment plugins

  Python

  •

  MIT License

  •1•0•0•2•Updated Aug 19, 2025Aug 19, 2025

• mastodon-release-post-action

  Public
  GitHub action to facilitate posting release notes on Mastodon

  Python

  •

  MIT License

  •0•0•0•2•Updated Aug 15, 2025Aug 15, 2025

• snakemake-image-kubeflow

  Public
  A Snakemake image for kubeflow

  Python

  •0•1•0•0•Updated Jul 30, 2025Jul 30, 2025

• snakemake-executor-plugin-cluster-sync

  Public
  A Snakemake executor plugin for generic cluster jobs that are executed synchronously.

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• snakemake-interface-report-plugins

  Public
  The interface for Snakemake report plugins.

  Python

  •

  MIT License

  •2•4•2•0•Updated Jul 29, 2025Jul 29, 2025

• snakemake-interface-storage-plugins

  Public
  This package provides a stable interface for interactions between Snakemake and its storage plugins.

  Python

  •

  MIT License

  •10•2•4•3•Updated Jul 29, 2025Jul 29, 2025

• snakemake-interface-executor-plugins

  Public
  This package provides a stable interface for interactions between Snakemake and its executor plugins.

  Python

  •

  MIT License

  •13•12•9•1•Updated Jul 29, 2025Jul 29, 2025

• snakemake-interface-scheduler-plugins

  Public
  This package provides a stable interface for interactions between Snakemake and its scheduler plugins.

  Python

  •

  MIT License

  •1•0•0•1•Updated Jul 29, 2025Jul 29, 2025

• snakedeploy

  Public
  deploy a snakemake pipeline directly from version control (under development)

  Python

  •

  Mozilla Public License 2.0

  •11•24•13•3•Updated Jul 28, 2025Jul 28, 2025

• snakemake-storage-plugin-s3

  Public
  A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)

  Python

  •

  MIT License

  •14•3•3•0•Updated Jul 25, 2025Jul 25, 2025

• snakemake-interface-logger-plugins

  Public
  Python

  •

  MIT License

  •1•3•0•1•Updated Jul 24, 2025Jul 24, 2025

• snakemake-interface-common

  Public
  Common functions and classes for Snakemake and its plugins

  Python

  •

  MIT License

  •4•0•2•1•Updated Jul 24, 2025Jul 24, 2025

• snakemake-executor-plugin-kubernetes

  Public
  A snakemake executor plugin for submission of jobs to Kubernetes

  Python

  •

  MIT License

  •9•4•2•5•Updated Jul 23, 2025Jul 23, 2025

• snakemake-tutorial-data

  Public
  Example data for the official Snakemake tutorial

  tutorialsnakemakereproducibility

  Dockerfile

  •23•9•0•2•Updated Jul 9, 2025Jul 9, 2025

• snakemake-lang-vscode-plugin

  Public
  Language support and snippets for Snakemake workflows (Snakefile, *.smk) for Visual Studio Code and Apache Theia.

  TypeScript

  •

  MIT License

  •16•20•10•1•Updated Jun 22, 2025Jun 22, 2025

• snakemake-github-action

  Public
  A Github action for running a Snakemake workflow

  MIT License

  •14•58•8•1•Updated Jun 15, 2025Jun 15, 2025

• snakemake-software-deployment-plugin-conda

  Public
  A Snakemake software deployment plugin for using conda packages. Implemented using py-rattler.

  Python

  •0•1•1•2•Updated Jun 11, 2025Jun 11, 2025

• snakemake-hpc-teaching-material

  Public
  TeX

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•1•2•Updated Jun 6, 2025Jun 6, 2025

• poetry-snakemake-plugin

  Public
  Plugin for poetry that adds snakemake specific functionality

  Python

  •2•6•0•2•Updated Jun 5, 2025Jun 5, 2025

• snakemake-storage-plugin-fs

  Public
  A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync.

  Python

  •

  MIT License

  •4•2•6•1•Updated May 15, 2025May 15, 2025

• snakemake-executor-plugin-googlebatch

  Public
  Snakemake executor plugin for Google Batch

  Python

  •

  MIT License

  •8•5•10•3•Updated Apr 8, 2025Apr 8, 2025

• snakemake-report-plugin-nanopub

  Public
  Snakemake Report Plugin to automatically create Nanopubs after workflow runs holding all metadata of that workflow

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

• snakemake-executor-plugin-slurm-jobstep

  Public
  A Snakemake executor plugin for running srun jobs inside of SLURM jobs (meant for internal use by snakemake-executor-plugin-slurm)

  Python

  •

  MIT License

  •3•0•1•0•Updated Mar 31, 2025Mar 31, 2025