Repositories list

• snakemake-wrappers

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

  Python

  •186•218•28•35•Updated Jan 31, 2025Jan 31, 2025

• snakemake

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

  snakemakereproducibilityworkflow-management

  HTML

  •

  MIT License

  •564•2.4k•1.1k•89•Updated Jan 31, 2025Jan 31, 2025

• snakemake-storage-plugin-s3

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

  Python

  •

  MIT License

  •11•2•3•4•Updated Jan 31, 2025Jan 31, 2025

• snakemake-interface-logger-plugins

  Public
  Python

  •0•0•0•1•Updated Jan 30, 2025Jan 30, 2025

• snakemake-hpc-teaching-material

  Public
  TeX

  •

  Creative Commons Attribution Share Alike 4.0 International

  •2•7•13•2•Updated Jan 30, 2025Jan 30, 2025

• snakemake-executor-plugin-aws-batch

  Public
  A Snakemake executor plugin for AWS Batch

  Python

  •

  MIT License

  •4•5•2•2•Updated Jan 29, 2025Jan 29, 2025

• snakemake-interface-software-deployment-plugins

  Public
  A stable interface for Snakemake software deployment plugins

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• snakemake.github.io

  Public
  Snakemake homepage

  snakemakehomepage

  HTML

  •

  MIT License

  •4•3•0•0•Updated Jan 28, 2025Jan 28, 2025

• snakemake-workflow-catalog

  Public
  A statically generated catalog of available Snakemake workflows

  HTML

  •

  MIT License

  •10•32•4•0•Updated Jan 27, 2025Jan 27, 2025

• snakemake-executor-plugin-slurm

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

  Python

  •

  MIT License

  •23•23•26•2•Updated Jan 25, 2025Jan 25, 2025

• snakemake-github-action

  Public
  A Github action for running a Snakemake workflow

  MIT License

  •12•56•14•0•Updated Jan 21, 2025Jan 21, 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

  •2•0•1•1•Updated Jan 13, 2025Jan 13, 2025

• snakefmt

  Public
  The uncompromising Snakemake code formatter

  pythonformatterfmt+ 5bioinformaticscodeblackcodeformattersnakemake

  Python

  •

  MIT License

  •29•155•15•2•Updated Jan 8, 2025Jan 8, 2025

• snakemake-storage-plugin-irods

  Public
  Snakemake storage plugin for handling input and output on iRODS

  Python

  •

  MIT License

  •3•0•1•3•Updated Dec 30, 2024Dec 30, 2024

• snakemake-interface-executor-plugins

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

  Python

  •

  MIT License

  •11•8•7•0•Updated Dec 21, 2024Dec 21, 2024

• snakemake-wrapper-utils

  Public
  Utility functions and classes shared between Snakemake wrappers

  Python

  •

  MIT License

  •7•3•0•3•Updated Dec 5, 2024Dec 5, 2024

• 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•3•0•Updated Nov 29, 2024Nov 29, 2024

• snakedeploy

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

  Python

  •

  Mozilla Public License 2.0

  •8•22•8•2•Updated Nov 27, 2024Nov 27, 2024

• poetry-snakemake-plugin

  Public
  Plugin for poetry that adds snakemake specific functionality

  Python

  •0•6•0•3•Updated Nov 6, 2024Nov 6, 2024

• snakemake-lang-vscode-plugin

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

  Python

  •

  MIT License

  •13•13•14•1•Updated Oct 20, 2024Oct 20, 2024

• snakemake-executor-plugin-kubernetes

  Public
  A snakemake executor plugin for submission of jobs to Kubernetes

  Python

  •

  MIT License

  •8•3•2•5•Updated Oct 8, 2024Oct 8, 2024

• snakemake-storage-plugin-gcs

  Public
  A Snakemake storage plugin for Google Cloud Storage

  Python

  •

  MIT License

  •5•4•0•2•Updated Oct 7, 2024Oct 7, 2024

• snakemake-interface-report-plugins

  Public
  The interface for Snakemake report plugins.

  Python

  •

  MIT License

  •0•3•0•0•Updated Oct 4, 2024Oct 4, 2024

• snakemake-interface-common

  Public
  Common functions and classes for Snakemake and its plugins

  Python

  •

  MIT License

  •3•0•1•0•Updated Oct 4, 2024Oct 4, 2024

• snakemake-executor-plugin-azure-batch

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

  Python

  •

  MIT License

  •1•2•2•1•Updated Sep 30, 2024Sep 30, 2024

• snakemake-interface-storage-plugins

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

  Python

  •

  MIT License

  •6•1•4•2•Updated Sep 20, 2024Sep 20, 2024

• snakemake-storage-plugin-xrootd

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

  Python

  •

  MIT License

  •2•0•2•0•Updated Sep 14, 2024Sep 14, 2024

• snakemake-executor-plugin-tes

  Public
  A Snakemake executor plugin for submitting jobs via GA4GH TES.

  Python

  •

  MIT License

  •2•0•2•4•Updated Sep 7, 2024Sep 7, 2024

• 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 Sep 7, 2024Sep 7, 2024

• snakemake-executor-plugin-google-lifesciences

  Public
  A Snakemake executor plugin for google lifesciences.

  Python

  •

  MIT License

  •2•0•1•1•Updated Sep 7, 2024Sep 7, 2024