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    69 repositories

    • 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
      •2•1•4•0•Updated Apr 24, 2026Apr 24, 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
      •635•2.8k•983•126•Updated Apr 24, 2026Apr 24, 2026

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •212•242•6•28•Updated Apr 24, 2026Apr 24, 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 Apr 23, 2026Apr 23, 2026

    • snakemake-storage-plugin-xrootd

      Public
      A Snakemake storage plugin for handling input and output via XRootD
      Python
      •
      MIT License
      •5•2•0•0•Updated Apr 23, 2026Apr 23, 2026

    • snakemake-workflow-catalog

      Public
      A statically generated catalog of available Snakemake workflows
      Python
      •
      MIT License
      •11•36•1•0•Updated Apr 22, 2026Apr 22, 2026

    • snakefmt

      Public
      The uncompromising Snakemake code formatter
      pythonformatterfmt
      pythonformatterfmtbioinformaticssnakemakecodeblackcodeformatter
      Python
      •
      MIT License
      •31•189•2•2•Updated Apr 20, 2026Apr 20, 2026

    • snakemake-executor-plugin-slurm

      Public
      A Snakemake executor plugin for submitting jobs to a SLURM cluster
      Python
      •
      MIT License
      •50•50•41•5•Updated Apr 17, 2026Apr 17, 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
      MIT License
      •0•1•0•0•Updated Apr 9, 2026Apr 9, 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•23•9•0•Updated Apr 2, 2026Apr 2, 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
      •6•0•0•1•Updated Apr 1, 2026Apr 1, 2026

    • snakemake-github-action

      Public
      A Github action for running a Snakemake workflow
      MIT License
      •15•62•1•3•Updated Mar 27, 2026Mar 27, 2026

    • snakemake-wasm-app

      Public
      Shell
      •0•1•0•0•Updated Mar 26, 2026Mar 26, 2026

    • snakemake-interface-report-plugins

      Public
      The interface for Snakemake report plugins.
      Python
      •
      MIT License
      •2•4•2•1•Updated Mar 25, 2026Mar 25, 2026

    • snakemake-wrapper-utils

      Public
      Utility functions and classes shared between Snakemake wrappers
      Python
      •
      MIT License
      •6•4•0•2•Updated Mar 24, 2026Mar 24, 2026

    • snakemake-scheduler-plugin-firstfit

      Public
      A Snakemake scheduler plugin that selects the first jobs that fit available resources.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • snakemake-interface-logger-plugins

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

    • snakemake-scheduler-plugin-milp

      Public
      A Snakemake scheduler plugin using Mixed-Integer Linear Programming (MILP).
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • snakemake-scheduler-plugin-greedy

      Public
      A greedy Snakemake scheduler plugin.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • snakemake-storage-plugin-http

      Public
      Snakemake storage plugin for donwloading input files from HTTP(s).
      Python
      •
      MIT License
      •4•1•3•4•Updated Mar 16, 2026Mar 16, 2026

    • snakemake-interface-storage-plugins

      Public
      This package provides a stable interface for interactions between Snakemake and its storage plugins.
      Python
      •
      MIT License
      •11•2•4•3•Updated Mar 16, 2026Mar 16, 2026

    • snakemake-interface-common

      Public
      Common functions and classes for Snakemake and its plugins
      Python
      •
      MIT License
      •7•0•6•5•Updated Mar 13, 2026Mar 13, 2026

    • snakemake-plugin-catalog

      Public
      An automatically updated catalog of Snakemake plugins and their documentation
      Python
      •
      MIT License
      •10•3•0•2•Updated Mar 13, 2026Mar 13, 2026

    • mastodon-release-post-action

      Public
      GitHub action to facilitate posting release notes on Mastodon
      Python
      •
      MIT License
      •0•0•0•2•Updated Mar 13, 2026Mar 13, 2026

    • snakeface

      Public
      The snakemake interface, currently works like a notebook (under development)
      CSS
      •
      Mozilla Public License 2.0
      •6•20•8•2•Updated Mar 12, 2026Mar 12, 2026

    • snakedeploy

      Public
      deploy a snakemake pipeline directly from version control (under development)
      snakemakereproducibility
      snakemakereproducibility
      Python
      •
      Mozilla Public License 2.0
      •13•25•14•7•Updated Mar 12, 2026Mar 12, 2026

    • snakemake-software-deployment-plugin-conda

      Public
      A Snakemake software deployment plugin for using conda packages. Implemented using py-rattler.
      Python
      •0•2•2•3•Updated Mar 10, 2026Mar 10, 2026

    • snakemake-interface-software-deployment-plugins

      Public
      A stable interface for Snakemake software deployment plugins
      Python
      •
      MIT License
      •1•0•1•0•Updated Mar 10, 2026Mar 10, 2026

    • snakemake-software-deployment-plugin-container

      Public
      Run snakemake within a rootless container
      Python
      •
      MIT License
      •1•2•0•1•Updated Mar 10, 2026Mar 10, 2026

    • snakemake-interface-executor-plugins

      Public
      This package provides a stable interface for interactions between Snakemake and its executor plugins.
      Python
      •
      MIT License
      •15•11•10•4•Updated Mar 9, 2026Mar 9, 2026
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