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    71 repositories

    • snakemake

      Public
      This is the development home of the workflow management system Snakemake. For general information, see
      snakemakereproducibilityworkflow-management
      snakemakereproducibilityworkflow-management
      Python
      •
      MIT License
      •648•2.8k•989•125•Updated May 25, 2026May 25, 2026

    • snakemake-workflow-catalog

      Public
      A statically generated catalog of available Snakemake workflows
      Python
      •
      MIT License
      •11•36•2•0•Updated May 25, 2026May 25, 2026

    • snakemake-executor-plugin-slurm

      Public
      A Snakemake executor plugin for submitting jobs to a SLURM cluster
      Python
      •
      MIT License
      •52•52•45•3•Updated May 23, 2026May 23, 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•2•Updated May 22, 2026May 22, 2026

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •210•244•7•31•Updated May 22, 2026May 22, 2026

    • snakefmt

      Public
      The uncompromising Snakemake code formatter
      pythonformatterfmt
      pythonformatterfmtbioinformaticssnakemakecodeblackcodeformatter
      Python
      •
      MIT License
      •31•191•2•2•Updated May 22, 2026May 22, 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 May 21, 2026May 21, 2026

    • snakemake-logger-plugin-github-status

      Public
      A Snakemake logger plugin that reports to the github commit status
      Python
      •0•0•0•0•Updated May 20, 2026May 20, 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•3•4•Updated May 19, 2026May 19, 2026

    • snakemake-software-deployment-plugin-eessi

      Public
      0•0•0•0•Updated May 13, 2026May 13, 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 May 13, 2026May 13, 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
      •0•1•0•0•Updated May 7, 2026May 7, 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
      •10•6•13•7•Updated Apr 27, 2026Apr 27, 2026

    • snakemake-executor-plugin-cluster-generic

      Public
      Generic cluster executor for Snakemake
      Python
      •
      MIT License
      •11•3•6•6•Updated Apr 27, 2026Apr 27, 2026

    • snakemake-storage-plugin-s3

      Public
      A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
      Python
      •
      MIT License
      •17•4•7•5•Updated Apr 27, 2026Apr 27, 2026

    • snakemake-github-action

      Public
      A Github action for running a Snakemake workflow
      MIT License
      •15•62•0•1•Updated Apr 24, 2026Apr 24, 2026

    • snakemake-wrapper-utils

      Public
      Utility functions and classes shared between Snakemake wrappers
      Python
      •
      MIT License
      •6•5•0•1•Updated Apr 24, 2026Apr 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
      •2•1•4•0•Updated Apr 24, 2026Apr 24, 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-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-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-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-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
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