Decorating and optimising a Snakemake workflow - October 2025 (3 of 5)

This video shows how to use configuration files to minimize the number of hardcoded parameters in a Snakemake workflow. The video also shows a simple way to process multiple files using the expand function, and finally how to allow jobs to use multiple cores. The video was recorded live during the course “Reproducible and Scalable Research with Snakemake and Software Containers” (https://www.sib.swiss/training/course...) streamed on 10 October 2025. Target audience: PhD students, postdoctoral and other researchers in the life sciences and bioinformaticians from both academia and industry who have an interest in increasing the reproducibility of their work. Speaker(s): Antonin Thiébaut, Centre Hospitalier Universitaire Vaudois, Switzerland. Rafael Riudavets Puig, ETH Zürich, Switzerland. 00:00 Introduction 01:09 Config files 09:46 Processing a list of files with the expand function 16:47 Multithreading Any questions about this video? Contact us training@sib.swiss