Snakemake Python Packages

snakemake

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

snakefmt

The uncompromising Snakemake code formatter

pytest-workflow

Configure workflow/pipeline tests using yaml files.

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.

turbo-picard

Picard-compatible Rust tools for faster SAM/BAM/CRAM, VCF, duplicate-marking and sequencing-QC workflows.

sequana

Sequana: a set of Snakemake NGS pipelines

workflow-canvas

Reproducible computational pipelines: containerized methods, content-addressed caching, run lineage, and a visual pipeline builder. Compiles to Snakemake.

snakebids

Snakemake + BIDS

monsda

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

snakedeploy

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

workflow-clinic

GA4GH Workflow Clinic

moduleultra

A control center for complex bioinformatics pipelines

fgsmk

Supporting Python functions for running Snakemake workflows

neurodent

Pipeline to analyze and generate figures from rodent EEGs

sequana-fastqc

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

panoptes-ui

Monitor computational workflows in real time

wfc-client

Reproducible computational pipelines: containerized methods, content-addressed caching, run lineage, and a visual pipeline builder. Compiles to Snakemake.

snek5000

:snake: Python framework for Nek5000 :rocket:

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.

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.

wbuild

R project report builder

cbicall

CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous computing environments.

rlpipes

RLPipes: A standardized R-loop-mapping pipeline.

snakemake-logger-plugin-pypsa

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