Pinned Repositories
shournal-to-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-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's Repositories
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-workflow-catalog
A statically generated catalog of available Snakemake workflows
snakemake/snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster
snakemake/snakemake-interface-executor-plugins
This package provides a stable interface for interactions between Snakemake and its executor plugins.
snakemake/snakemake-hpc-teaching-material
snakemake/snakemake-executor-plugin-aws-batch
A Snakemake executor plugin for AWS Batch
snakemake/snakemake-storage-plugin-gcs
A Snakemake storage plugin for Google Cloud Storage
snakemake/snakemake-executor-plugin-googlebatch
Snakemake executor plugin for Google Batch
snakemake/snakemake-interface-report-plugins
The interface for Snakemake report plugins.
snakemake/poetry-snakemake-plugin
Plugin for poetry that adds snakemake specific functionality
snakemake/snakemake-executor-plugin-kubernetes
A snakemake executor plugin for submission of jobs to Kubernetes
snakemake/snakemake-storage-plugin-fs
A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync.
snakemake/snakemake-storage-plugin-s3
A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
snakemake/snakemake-executor-plugin-azure-batch
A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch.
snakemake/snakemake-executor-plugin-cluster-generic
Generic cluster executor for Snakemake
snakemake/snakemake-executor-plugin-drmaa
A snakemake executor plugin for submission of jobs via DRMAA.
snakemake/snakemake-executor-plugin-flux
Snakemake custom executor plugin for Flux Framework (under development)
snakemake/snakemake-interface-storage-plugins
This package provides a stable interface for interactions between Snakemake and its storage plugins.
snakemake/snakemake-storage-plugin-azure
Snakemake storage plugin for Azure Blob Storage
snakemake/snakemake-executor-plugin-cluster-sync
A Snakemake executor plugin for generic cluster jobs that are executed synchronously.
snakemake/snakemake-executor-plugin-google-lifesciences
A Snakemake executor plugin for google lifesciences.
snakemake/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/snakemake-executor-plugin-tes
A Snakemake executor plugin for submitting jobs via GA4GH TES.
snakemake/snakemake-interface-common
Common functions and classes for Snakemake and its plugins
snakemake/snakemake-storage-plugin-http
Snakemake storage plugin for donwloading input files from HTTP(s).
snakemake/snakemake-storage-plugin-irods
Snakemake storage plugin for handling input and output on iRODS
snakemake/snakemake-storage-plugin-webdav
A Snakemake storage plugin for handling input and output via webdav
snakemake/snakemake-storage-plugin-xrootd
A Snakemake storage plugin for handling input and output via XRootD