Projects in Awesome Lists by snakemake

https://github.com/snakemake/snakemake

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

reproducibility snakemake workflow-management

Last synced: 29 Jan 2026

https://github.com/snakemake/snakemake-wrappers

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

Last synced: 25 Feb 2026

https://github.com/snakemake/snakefmt

The uncompromising Snakemake code formatter

bioinformatics black code codeformatter fmt formatter python snakemake

Last synced: 09 Feb 2026

https://github.com/snakemake/snakemake-github-action

A Github action for running a Snakemake workflow

Last synced: 16 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster

Last synced: 06 Oct 2025

https://github.com/snakemake/snakemake-workflow-catalog

A statically generated catalog of available Snakemake workflows

Last synced: 26 Jun 2026

https://github.com/snakemake/snakeface

The snakemake interface, currently works like a notebook (under development)

Last synced: 21 Apr 2025

https://github.com/snakemake/snakedeploy

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

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-lang-vscode-plugin

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

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-interface-executor-plugins

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

Last synced: 21 Apr 2025

https://github.com/snakemake/shournal-to-snakemake

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-aws-batch

A Snakemake executor plugin for AWS Batch

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-hpc-teaching-material

Last synced: 16 Mar 2026

https://github.com/snakemake/snakemake-tutorial-data

Example data for the official Snakemake tutorial

reproducibility snakemake tutorial

Last synced: 26 Jun 2026

https://github.com/snakemake/snakemake-tutorials

start of repository with various snakemake tutorials (under development)

google-cloud snakemake snakemake-tutorials tutorials under-development

Last synced: 27 Feb 2026

https://github.com/snakemake/snakemake-executor-plugin-kueue

A Snakemake executor plugin to enable running jobs with Kueue on Kubernetes

Last synced: 21 Apr 2025

https://github.com/snakemake/poetry-snakemake-plugin

Plugin for poetry that adds snakemake specific functionality

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-spack-tutorial

The snakemake tutorial run with spack! (under development)

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-storage-plugin-gcs

A Snakemake storage plugin for Google Cloud Storage

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-googlebatch

Snakemake executor plugin for Google Batch

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-cluster-generic

Generic cluster executor for Snakemake

Last synced: 14 Jun 2025

https://github.com/snakemake/snakemake-wrapper-utils

Utility functions and classes shared between Snakemake wrappers

Last synced: 06 Nov 2025

https://github.com/snakemake/snakemake-interface-report-plugins

The interface for Snakemake report plugins.

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-kubernetes

A snakemake executor plugin for submission of jobs to Kubernetes

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake.github.io

Snakemake homepage

homepage snakemake

Last synced: 02 Mar 2026

https://github.com/snakemake/snakemake-interface-logger-plugins

Last synced: 02 Jul 2025

https://github.com/snakemake/snakemake-storage-plugin-zenodo

A Snakemake storage plugin for zenodo

Last synced: 09 Mar 2026

https://github.com/snakemake/snakemake-executor-plugin-azure-batch

A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch.

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-storage-plugin-s3

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

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-object

Language agnostic encoding of Snakemake job information as 'Snakemake objects' into Snakemake script preambles

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-lsh-tutorial-data

Data for the Snakemake Google life science executor tutorial

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-plugin-catalog

An automatically updated catalog of Snakemake plugins and their documentation

Last synced: 21 Apr 2025

https://github.com/snakemake/snakedeploy-github-action

A github action for using snakedeploy

Last synced: 26 Jun 2026

https://github.com/snakemake/snakemake-storage-plugin-fs

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

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-interface-storage-plugins

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

Last synced: 20 Feb 2026

https://github.com/snakemake/snakemake-software-deployment-plugin-conda

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

Last synced: 18 Feb 2026

https://github.com/snakemake/snakemake-storage-plugin-apd

Snakemake storage plugin for use with the LHCb apd package

Last synced: 12 Oct 2025

https://github.com/snakemake/snakemake-executor-plugin-drmaa

A snakemake executor plugin for submission of jobs via DRMAA.

Last synced: 03 Jan 2026

https://github.com/snakemake/snakemake-image-kubeflow

A Snakemake image for kubeflow

Last synced: 02 Jul 2025

https://github.com/snakemake/snakemake-executor-plugin-flux

Snakemake custom executor plugin for Flux Framework (under development)

flux flux-framework snakemake

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-storage-plugin-xrootd

A Snakemake storage plugin for handling input and output via XRootD

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-ssh

An experimental Snakemake remote executor plugin that only requires ssh

Last synced: 02 Jul 2025

https://github.com/snakemake/snakemake-software-deployment-plugin-container

Run snakemake within a rootless container

Last synced: 17 Feb 2026

https://github.com/snakemake/snakemake-executor-plugin-cluster-sync

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

Last synced: 31 Oct 2025

https://github.com/snakemake/snakemake-report-plugin-nanopub

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

Last synced: 29 Oct 2025

https://github.com/snakemake/snakemake-storage-plugin-ftp

A Snakemake storage plugin that handles files and directories on an FTP server

Last synced: 19 Jul 2025

https://github.com/snakemake/snakemake-storage-plugin-azure

Snakemake storage plugin for Azure Blob Storage

Last synced: 05 Apr 2025

https://github.com/snakemake/snakemake-executor-plugin-tes

A Snakemake executor plugin for submitting jobs via GA4GH TES.

Last synced: 17 Feb 2026

https://github.com/snakemake/snakemake-storage-plugin-http

Snakemake storage plugin for donwloading input files from HTTP(s).

Last synced: 21 Apr 2025

https://github.com/snakemake/snakemake-interface-software-deployment-plugins

A stable interface for Snakemake software deployment plugins

Last synced: 02 Jun 2026

https://github.com/snakemake/snakemake-scheduler-plugin-greedy

A greedy Snakemake scheduler plugin.

Last synced: 01 Apr 2026

https://github.com/snakemake/snakemake-storage-plugin-irods

Snakemake storage plugin for handling input and output on iRODS

Last synced: 05 Mar 2026

https://github.com/snakemake/snakemake-plugin-docs-example

An example documentation site for a plugin using snakemake-plugin-docs-jekyll

snakemake snakemake-plugin snakemake-theme

Last synced: 12 Jun 2026

https://github.com/snakemake/snakemake-plugin-docs-jekyll

Jekyll template for snakemake plugins (under development)!

Last synced: 31 May 2026

https://github.com/snakemake/mastodon-release-post-action

GitHub action to facilitate posting release notes on Mastodon

Last synced: 04 Jun 2026

https://github.com/snakemake/snakemake-storage-plugin-webdav

A Snakemake storage plugin for handling input and output via webdav

snakemake-plugin webdav

Last synced: 10 Mar 2026