Snakemake

snakedeploy

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

snakeface

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

snakefmt

The uncompromising Snakemake code formatter

snakemake

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

snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster

snakemake-github-action

A Github action for running a Snakemake workflow

snakemake-interface-executor-plugins

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

snakemake-lang-vscode-plugin

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

snakemake-workflow-catalog

A statically generated catalog of available Snakemake workflows

snakemake-wrappers

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

snakemake/snakemake

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

snakemake/snakemake-wrappers

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

snakemake/snakefmt

The uncompromising Snakemake code formatter

snakemake/snakemake-github-action

A Github action for running a Snakemake workflow

snakemake/snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster

snakemake/snakemake-workflow-catalog

A statically generated catalog of available Snakemake workflows

snakemake/snakedeploy

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

snakemake/snakemake-lang-vscode-plugin

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

snakemake/snakemake-interface-executor-plugins

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

snakemake/snakemake-tutorial-data

Example data for the official Snakemake tutorial

snakemake/snakemake-hpc-teaching-material

snakemake/poetry-snakemake-plugin

Plugin for poetry that adds snakemake specific functionality

snakemake/snakemake-wrapper-utils

Utility functions and classes shared between Snakemake wrappers

snakemake/snakemake-executor-plugin-kubernetes

A snakemake executor plugin for submission of jobs to Kubernetes

snakemake/snakemake-interface-logger-plugins

snakemake/snakemake-interface-report-plugins

The interface for Snakemake report plugins.

snakemake/snakemake-plugin-catalog

An automatically updated catalog of Snakemake plugins and their documentation

snakemake/snakemake-storage-plugin-s3

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

snakemake/snakemake.github.io

Snakemake homepage

snakemake/snakemake-interface-storage-plugins

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

snakemake/snakemake-storage-plugin-fs

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

snakemake/snakemake-image-kubeflow

A Snakemake image for kubeflow

snakemake/snakemake-software-deployment-plugin-conda

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

snakemake/snakemake-storage-plugin-xrootd

A Snakemake storage plugin for handling input and output via XRootD

snakemake/mastodon-release-post-action

GitHub action to facilitate posting release notes on Mastodon

snakemake/snakemake-executor-plugin-cluster-sync

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

snakemake/snakemake-interface-common

Common functions and classes for Snakemake and its plugins

snakemake/snakemake-interface-scheduler-plugins

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

snakemake/snakemake-interface-software-deployment-plugins

A stable interface for Snakemake software deployment plugins

snakemake/snakemake-software-deployment-plugin-envmodules

Snakemake software deployment plugin for environment modules