Particle Physics Seminar

Transparency, reproducibility and the democratization of an ecosystem – the benefits of Snakemake 8

by Prof. Johannes Köster (Universität Duisburg-Essen)

CP-03-123 (TU Dortmund)


TU Dortmund

Otto-Hahn-Straße 4a 44227 Dortmund

The Snakemake workflow management system is a tool to create reproducible, scalable, transparent, and adaptable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

With over 1 million downloads, and on average over 11 new citations per week (>2000 in total), Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications and is used in many important projects, from shaping our knowledge of the human genome, to virus surveillance during the SARS-CoV-2 pandemic, to particle physics at CERN.

This talk will briefly introduce Snakemake, followed by detailed insights into recent ecosystem advances and best practices.

Organized by

Maik Becker & Serena Maccolini