Snakemake tutorial

The Snakemake BYOC (bring-your-own-code) workshop is a follow-up on the NBIS Tools for reproducible research course and we therefore expect all participants to be familiar with the material from the Snakemake tutorial (link to the latest version).

Please take some time to go through the material before the workshop in case you didn't work with Snakemake in a while.

Workshop structure

The workshop is split into short lectures, feedback sessions and coding sessions. We will work in small groups during the workshop that will each have their own teacher. During the coding sessions, you will have time to work on your Snakemake workflow. A teacher and maximum three other participants will be online with you for questions during these coding sessions. We will try to match the participants in each group according to their experience levels and aims based on the responses on the application form.

"Bring-your-own-code" project presentations

During the feedback session on the first day, you will be asked to present your "bring-your-own-code" project to your group so that you can receive feedback to make sure you have a good starting point to work on your project during the workshop.

Each participant will get in total 30 minutes for the presentation and for questions and feedback. The aim of this presentation is to make everyone in your group (including your teacher) familiar with the code that you will work on during the workshop so that you can get the best possible help. Therefore, please only give a very short introduction to the research question and focus the remaining presentation on the actual code and analysis steps of your project.

Computational requirements

The participants are expected to work on a computer with a functioning webcam, preferably with Linux or Mac installed (you will be asked for your operating system in the application form). If you haven't used Snakemake on this computer yet, please make sure you have installed Snakemake before the workshop.

If you are planning to use a computer with Windows 10, please follow the setup instructions for Windows users from the NBIS Tools for reproducible research course to install the Linux bash shell.

The workshop is held entirely online using Zoom. Please download and install Zoom and test your sound and webcam before the workshop starts as we want to make sure we can see and hear each other during the workshop.

If you already have a Zoom installation, please update it to the latest version.