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Snakemake BYOC (bring-your-own-code) workshop (ONLINE)


Online event via Zoom
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Snakemake BYOC (bring-your-own-code) workshop (ONLINE)

August 31, 2022 @ 09:00 September 2, 2022 @ 13:00 CEST

National workshop open for PhD students (prioritized), postdocs, researchers and others from all Swedish universities who have previously participated in the NBIS Tools for reproducible research course or with demonstrated experience in writing Snakemake workflows.

Important dates

Application opens:  May 15

Application closes: June 17

Confirmation to accepted students:  June 28

Responsible teachers:  Verena Kutschera, John Sundh, Per Unneberg, Marcel Martin

Contact information: edu.byoc-snakemake@nbis.se

Workshop fee

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 1,700 SEK.

*Please note that NBIS cannot invoice individuals

Workshop 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

After participation in the BYOC workshop, participants will:

  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 workshop. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflows
  • 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). You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the workshop.

The workshop can accommodate a maximum of 16 participants. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.