Snakemake Python Packages

snakemake

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

pytest-workflow

Configure workflow/pipeline tests using yaml files.

snakefmt

The uncompromising Snakemake code formatter

tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

panoptes-ui

Monitor computational workflows in real time

sequana

Sequana: a set of Snakemake NGS pipelines

workflow-clinic

GA4GH Workflow Clinic

snakedeploy

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

snakebids

Snakemake + BIDS

snakesee

A terminal UI for monitoring Snakemake workflows

monsda

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

snakevision

An awesome tool to visualize snakemake rule graphs

moduleultra

Tools to make pipelines easier to run and distribute for large biological datasets

sequana-fastqc

sequana pipeline to perform parallel fastqc and summarize results with multiqc plot

metasheet-guard

Experimental-design-aware quality control for sequencing analysis sample sheets.

snakemake-storage-plugin-cached-http

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

pubrunner

A framework to rerun text mining tools on the latest publications

nbpipeline

Snakemake-like pipeline manager for reproducible Jupyter Notebooks

snek5000

Python framework for Nek5000

snakemake-logger-plugin-pypsa

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

sunbeamlib

A robust, extensible metagenomics pipeline

hecatomb

Viral metagenomics framework for short and longreads

snakemake-executor-plugin-pcluster-slurm

A Snakemake executor plugin for submitting jobs to an AWS Parallel Cluster (pcluster) SLURM cluster.

solida

NGS pipelines bootstrapper