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.

sequana

Sequana: a set of Snakemake NGS pipelines

snakebids

Snakemake + BIDS

sequana-fastqc

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

monsda

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

moduleultra

A control center for complex bioinformatics pipelines

snakevision

A tool to visualize Snakemake workflows.

snakemake-storage-plugin-lfs

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

snakedeploy

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

solida

SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

snek5000

:snake: Python framework for Nek5000 :rocket:

hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

rlpipes

A standardized R-loop-mapping pipeline

snakemake-executor-plugin-pcluster-slurm

slurm executor for use by snakemake when running on the slurm flavor which is unique to aws parallel cluster slrum pcluster.

snakedoc

A Sphinx extension for Snakemake workflows

pnnl-atlas

ATLAS - Three commands to start analyzing your metagenome data

pubrunner

A framework for keeping biomedical text mining result up-to-date

sunbeamlib

A snakemake utility for metagenomic sequencing analysis

ymp

Flexible multi-omic pipeline system

nbpipeline

Snakemake-like pipeline manager for reproducible Jupyter Notebooks

snakemake-storage-plugin-cached-http

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