Snakemake BYOC (bring-your-own-code) 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

Links to an external site. 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

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

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

Pre-requisites

• 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 macOS (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.

Level

beginner