Course syllabus


31 August - 2 September 2022
Online (zoom link)


Audience Workshop open for PhD students (prioritized), postdocs, researchers and others who have previously participated in the NBIS Tools for reproducible research course or with demonstrated experience in writing Snakemake workflows.

Fee This online training event has no fee. However, if you confirm your participation but do not do so (no-show) you will be invoiced 1,700 SEK. Please note that NBIS cannot invoice individuals.

By accepting to participate in the course, you will be agreeing to follow the NBIS Training Code of Conduct.


Teachers & contact

Verena Kutschera, John Sundh, Per Unneberg, Marcel Martin

Email address


Workshop description

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 bioinformatic workflows. The NBIS Tools for reproducible research course is held twice a year and provides both an introduction to Snakemake and a tutorial on how to use it.

This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to

  1. convert their data analysis from a programming language such as bash, R or Python into a Snakemake workflow, OR
  2. apply more advanced techniques to their existing Snakemake workflows.


Learning outcomes

At the end of the workshop, participants should be able to:

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



Entry requirements
  • Previous participation in the NBIS Tools for reproducible research course. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.).
  • 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, ideally running Linux or Mac OS (if you run Windows and are interested in participating please note that this will require a specific setup, see the pre-workshop information). You will be asked to install the video conferencing software Zoom to be able to participate in the workshop.


Due to limited space the workshop can accommodate maximum of 16 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance.

This is a national workshop. The workshop is open for PhD students, postdocs, group leaders and core facility staff. We do accept application from other countries, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a workshop application in order to establish whether the workshop is valid for formal credits or not.


Follow this link to apply

Important dates:

  • Application opens: May 15
  • Application deadline: June 17
  • Confirmation to accepted participants: June 28



The workshop schedule can be found here.


Pre-workshop information

Please read the pre-workshop information carefully before the workshop starts and follow the instructions there to prepare for the workshop.