Snakemake

snakemake

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

snakemake-wrappers

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

snakefmt

The uncompromising Snakemake code formatter

snakemake-workflow-catalog

A statically generated catalog of available Snakemake workflows

snakedeploy

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

snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster

snakemake-interface-executor-plugins

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

snakemake-executor-plugin-kueue

A Snakemake executor plugin to enable running jobs with Kueue on Kubernetes

snakemake.github.io

Snakemake homepage

snakemake-executor-plugin-aws-batch

A Snakemake executor plugin for AWS Batch

snakemake-executor-plugin-kubernetes

A snakemake executor plugin for submission of jobs to Kubernetes

snakemake-hpc-teaching-material

snakemake-storage-plugin-gcs

A Snakemake storage plugin for Google Cloud Storage

poetry-snakemake-plugin

Plugin for poetry that adds snakemake specific functionality

snakemake-executor-plugin-azure-batch

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

snakemake-executor-plugin-cluster-generic

Generic cluster executor for Snakemake

snakemake-executor-plugin-drmaa

A snakemake executor plugin for submission of jobs via DRMAA.

snakemake-executor-plugin-flux

Snakemake custom executor plugin for Flux Framework (under development)

snakemake-executor-plugin-googlebatch

Snakemake executor plugin for Google Batch (under development)

snakemake-interface-storage-plugins

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

snakemake-storage-plugin-fs

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

snakemake-executor-plugin-cluster-sync

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

snakemake-executor-plugin-slurm-jobstep

A Snakemake executor plugin for running srun jobs inside of SLURM jobs (meant for internal use by snakemake-executor-plugin-slurm)

snakemake-executor-plugin-tes

A Snakemake executor plugin for submitting jobs via GA4GH TES.

snakemake-interface-common

Common functions and classes for Snakemake and its plugins

snakemake-plugin-catalog

An automatically updated catalog of Snakemake plugins and their documentation

snakemake-storage-plugin-http

Snakemake storage plugin for donwloading input files from HTTP(s).

snakemake-storage-plugin-irods

Snakemake storage plugin for handling input and output on iRODS

snakemake-storage-plugin-s3

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

snakemake-storage-plugin-xrootd

A Snakemake storage plugin for handling input and output via XRootD