Snakemake Python Packages

snakemake

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

284K 3K 645

pytest-workflow

Configure workflow/pipeline tests using yaml files.

57K 69 10

snakefmt

The uncompromising Snakemake code formatter

23K 189 31

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.

11K 72 28

sequana

Sequana: a set of Snakemake NGS pipelines

3K 151 27

snakedoc

A Sphinx extension for Snakemake workflows

3K 9 1

snakebids

Snakemake + BIDS

2K 22 16

monsda

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

2K 12 3

moduleultra

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

1K 1 1

snakevision

An awesome tool to visualize snakemake rule graphs

1K 34 1

snakemake-storage-plugin-lfs

Snakemake storage plugin for downloading Git LFS files with optional local caching

841 572 417

snakedeploy

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

810 25 13

sequana-fastqc

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

682 5 3

snek5000

:snake: Python framework for Nek5000 :rocket:

659 31 11

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.

574 6 1