Snakemake “bring-your-own-code” (BYOC) workshop


Online event via Zoom

Snakemake “bring-your-own-code” (BYOC) workshop

May 27, 2024 @ 08:00 May 29, 2024 @ 17:00 CEST

National workshop open for PhD students (prioritized), postdocs, researchers and other employees at Swedish universities in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. This workshop requires previous participation in the NBIS Tools for reproducible research course or experience in writing Snakemake workflows.

Important dates and information

Application opens: 2024-02-26

Application closes: 2024-04-14

Confirmation to accepted students: 2024-04-22

Course Leader and teachers: Verena Kutschera (CL), Marcel Martin, John Sundh, Per Unneberg

In case you have any workshop-specific questions, please contact:

Course fee

This online training event has no fee. However, if you confirm your participation but do not show up (no-show) you will be invoiced 2,000 SEK*.

*Please note that NBIS cannot invoice individuals

Course content

As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up, perform and monitor defined sequences of computational tasks (“workflows”), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows.

The NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake.

This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash, R or python into a Snakemake workflow, or B) apply more advanced techniques to their existing Snakemake workflows.

Learning Outcomes

Upon completion of this course, you will be able to:

  • Be able to create Snakemake workflows for bioinformatics data analysis
  • Demonstrate knowledge of the structure and syntax of different types of Snakemake workflows
  • Demonstrate knowledge of advanced features of the Snakemake workflow language

Entry requirements

The following is a list of skills required for being able to follow the course:

  • Previous participation in the NBIS Tools for reproducible research course. The workshop is also open for participants with experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with the command line and commands such as ls, cd, touch, mkdir, pwd, wget, etc.). We will use the information you provide in the application form to assess your Snakemake and Unix/bash knowledge.
  • Your own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improve. 
  • A computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant, additional setup will be required).

Due to limited space the course can accommodate a maximum of 16 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

Last updated: 2024-02-21

Content Responsible: Hampus Persson(