Reproducible and Scalable Research with Snakemake and Software Containers

Overview

Reproducibility in research is essential to validate scientific findings and build upon them. In the context of data analysis, this involves not only making code publicly available but also transparently communicating the specific software libraries and tools used in the analysis. To achieve this level of transparency and consistency, this course introduces the Snakemake workflow management system combined with software containers. Very briefly, workflow management systems are designed to create reproducible and scalable analysis pipelines, streamlining the process of managing complex computational tasks. Software containers are very powerful tools to ensure the same software is used across different computational platforms. By combining workflow management systems with software containers, the participants will learn a robust approach to maintaining both reproducibility and scalability in their data analysis projects, setting a strong foundation for reproducible scientific research.

Audience

This course is addressed to all bioinformaticians developing computational pipelines with an interest to increase the reproducibility of their work.

Learning outcomes

At the end of the course, the participants are expected to:

• Understand the basic principles and advantages of workflow management systems.

• Create data analysis pipelines with Snakemake.

• Combine Snakemake with containers to build reproducible computational pipelines.

• Run Snakemake pipelines locally and in HPC environments.

Prerequisites

Knowledge / competencies

This course is addressed to bioinformaticians with a basic to medium knowledge of UNIX commands. In addition, participants are expected to either have participated in one of our container courses or have a good knowledge of software containers.

Technical

Participants are required to bring their own laptop with an installed modern code editor such as VScode.

Schedule - CET time zone

09:00 – 09:45: introduction to workflow management systems.

09:45 – 10:15: building a simple analysis pipeline with Snakemake.

10:15 – 10:30: break.

10:30 – 11:15: using wildcards to increase scalability.

11:15 – 12:00: updating the analysis pipeline to increase scalability.

12:00 – 13:00: lunch break.

13:00 – 13:30: using configuration files to increase transferability.

13:30 – 14:00: complementing our workflow with a configfile.

14:00 – 14:30: combining Snakemake with conda and software containers.

14:30 – 15:15: updating the analysis pipeline to use conda/containers.

15:15 – 15:30: break.

15:30 – 16:15: Snakemake in HPC environments.

16:15 – 17:00: updating our workflow to send jobs via SLURM.

Application

The registration fees for academics are 100 CHF and 500 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications will close on 26/09/2025 or as soon as the places will be filled up. Deadline for free-of-charge cancellation is set to 26/09/2025. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

The course will be held in Bern.

The course will start at 9:15 and end around 17:15.

More information will be provided to the registered participants in due time.

Additional information

Coordination: Patricia Palagi, SIB Training team.

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.