Being reproducible with Snakemake - October 2025 (4 of 5)

This video shows how to significantly increase the reproducibility of a Snakemake workflow by using Conda and software containers. The lecture also shows how to run scripts from other languages in combination with Snakemake, and how to use input functions to deal with cases where we don’t know the number of input files. 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 01:13 Using Conda with Snakemake 04:35 Using containers with Snakemake 10:38 Running scripts from other languages 14:38 Input functions 22:43 Checkpoints Any questions about this video? Contact us training@sib.swiss