snakemake

A GA4GH compliant Workflow-Execution-Service (WES) for Nextflow and Snakemake.

AUMC RNAseq pipeline A snakemake made to perform QC + alignement + quantifications of reads coming from RNAseq experiments.

Deployment code for WESkit based on Docker-Swarm.

IMPORTANT: (1) This is for development only, (2) is not maintained and will be archived to be replaced by the k8s/helm deployment.

Projet réalisé dans le cadre de l'UE - Calculs parallèles et Programmation GPU, visant le retraitement des données de DNAse-seq produites par Gomez-Cabrero et al. en 2019 (https://doi.org/10.1038/s41597-019-0202-7) avec une approche snakemake sous serveur HPC.

ARpip

This project shows an example of how a collaborative collected FAIR dataset can be extended (using Merge Requests), curated (using automated testing), analyzed (using a Snakemake workflow), and visualized (using Python).

Provides basic language support and snippets for Snakemake files (Snakefile, .smk) to Visual Studio Code. https://marketplace.visualstudio.com/items?itemName=alping.vscode-snakemake

Snakemake RNAseq processing pipeline (STAR or Salmon) via a SLURM cluster

A cookiecutter template for Snakemake workflows