Repositories list

• snakemake-hpc-teaching-material

  Public
  TeX

  •

  Creative Commons Attribution Share Alike 4.0 International

  •2•0•1•0•Updated Dec 9, 2025Dec 9, 2025

• snakemake

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

  snakemakereproducibilityworkflow-management

  Python

  •

  MIT License

  •618•2.7k•1.1k•82•Updated Dec 9, 2025Dec 9, 2025

• snakemake-workflow-catalog

  Public
  A statically generated catalog of available Snakemake workflows

  Python

  •

  MIT License

  •10•36•2•0•Updated Dec 9, 2025Dec 9, 2025

• snakemake-executor-plugin-slurm

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

  Python

  •

  MIT License

  •40•44•41•7•Updated Dec 8, 2025Dec 8, 2025

• snakemake-github-action

  Public
  A Github action for running a Snakemake workflow

  MIT License

  •15•62•5•4•Updated Dec 5, 2025Dec 5, 2025

• snakemake-wrappers

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

  Python

  •203•237•14•34•Updated Dec 5, 2025Dec 5, 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 Dec 1, 2025Dec 1, 2025

• mastodon-release-post-action

  Public
  GitHub action to facilitate posting release notes on Mastodon

  Python

  •

  MIT License

  •0•0•0•1•Updated Nov 30, 2025Nov 30, 2025

• snakedeploy

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

  snakemakereproducibility

  Python

  •

  Mozilla Public License 2.0

  •13•24•14•5•Updated Nov 26, 2025Nov 26, 2025

• snakemake-plugin-catalog

  Public
  An automatically updated catalog of Snakemake plugins and their documentation

  Python

  •

  MIT License

  •6•3•2•2•Updated Nov 19, 2025Nov 19, 2025

• snakemake-scheduler-plugin-firstfit

  Public
  A Snakemake scheduler plugin that selects the first jobs that fit available resources.

  Python

  •

  MIT License

  •1•0•0•1•Updated Nov 18, 2025Nov 18, 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

  •5•0•0•1•Updated Nov 10, 2025Nov 10, 2025

• snakemake-executor-plugin-kubernetes

  Public
  A snakemake executor plugin for submission of jobs to Kubernetes

  Python

  •

  MIT License

  •11•4•2•5•Updated Nov 10, 2025Nov 10, 2025

• snakemake-interface-report-plugins

  Public
  The interface for Snakemake report plugins.

  Python

  •

  MIT License

  •2•4•2•0•Updated Oct 31, 2025Oct 31, 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•0•Updated Oct 31, 2025Oct 31, 2025

• snakefmt

  Public
  The uncompromising Snakemake code formatter

  pythonformatterfmt+ 5bioinformaticssnakemakecodeblackcodeformatter

  Python

  •

  MIT License

  •32•181•13•1•Updated Oct 29, 2025Oct 29, 2025

• snakemake-interface-scheduler-plugins

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

  Python

  •

  MIT License

  •2•0•0•0•Updated Oct 20, 2025Oct 20, 2025

• snakedeploy-github-action

  Public
  A github action for using snakedeploy

  Dockerfile

  •

  MIT License

  •2•2•0•0•Updated Oct 6, 2025Oct 6, 2025

• snakemake.github.io

  Public
  Snakemake homepage

  snakemakehomepage

  HTML

  •

  MIT License

  •3•3•0•0•Updated Oct 1, 2025Oct 1, 2025

• snakemake-interface-software-deployment-plugins

  Public
  A stable interface for Snakemake software deployment plugins

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 1, 2025Oct 1, 2025

• snakemake-interface-common

  Public
  Common functions and classes for Snakemake and its plugins

  Python

  •

  MIT License

  •5•0•3•4•Updated Sep 30, 2025Sep 30, 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

  •17•22•9•1•Updated Sep 30, 2025Sep 30, 2025

• snakemake-interface-executor-plugins

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

  Python

  •

  MIT License

  •14•11•10•3•Updated Sep 30, 2025Sep 30, 2025

• snakemake-interface-logger-plugins

  Public
  Python

  •

  MIT License

  •2•7•1•3•Updated Sep 28, 2025Sep 28, 2025

• snakemake-storage-plugin-xrootd

  Public
  A Snakemake storage plugin for handling input and output via XRootD

  Python

  •

  MIT License

  •3•1•1•1•Updated Sep 22, 2025Sep 22, 2025

• snakemake-software-deployment-plugin-envmodules

  Public
  Snakemake software deployment plugin for environment modules

  Python

  •1•0•0•0•Updated Sep 19, 2025Sep 19, 2025

• snakemake-software-deployment-plugin-conda

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

  Python

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

• snakemake-wrapper-utils

  Public
  Utility functions and classes shared between Snakemake wrappers

  Python

  •

  MIT License

  •7•4•0•1•Updated Sep 11, 2025Sep 11, 2025

• snakemake-storage-plugin-s3

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

  Python

  •

  MIT License

  •16•4•7•3•Updated Sep 11, 2025Sep 11, 2025

• snakemake-image-kubeflow

  Public
  A Snakemake image for kubeflow

  Python

  •0•1•0•1•Updated Sep 9, 2025Sep 9, 2025