Reproducible analysis workflows with Snakemake and Conda (2021-07-14)

14 July 2021 - 16 July 2021 three days, Online Register here


In this practical course you will learn how to write and run reproducible and scalable data analysis workflows using the Snakemake workflow engine. You will also learn how to manage packages and software required for your workflow using the Conda package manager and how to isolate installations in virtual environments.

Besides a short introduction lecture, the course will consist mostly of hands-on practical sessions.

The course will be held online using Webex platform over three half-days from July 14th - July 16th, 2021 09:30-12:30 am.

PhD students will be awarded with 0.5 ECTS upon successful completion of the training assignments.


  • Laptop or desktop PC
  • Webex and a microphone
  • Ability and permission to install a virtual machine on your laptop/PC, or alternative access to a Linux system
  • Basic knowledge of the Linux command-line (executing commands, navigating files and folders, writing files with a command-line editor)
  • (Optional) To fully benefit from the HPC part, you will need access to an HPC cluster with the SLURM scheduler and some experience how to run jobs on it

Additionally, a few days before the course, detailed instructions on what to prepare will be sent out to confirmed participants.


Registration is open with limited places. Participation is on a first come, first served basis.

Time Plan (Preliminary agenda)

Wednesday 14 July 2021

Time Topic
09:30 - 09:45 Welcome and introduction round.
09:45 - 10:30 Introduction to Conda, Snakemake and our example workflow.
10:30 - 11:00 Installing Conda and Snakemake.
11:00 - 12:30 First steps in Snakemake.

Thursday 15 July 2021

Time Topic
09:30 - 12:30 Creating and running the example workflow in Snakemake

Friday 16 July 2021

Time Topic
09:30 - 11:00 Scaling up and using snakemake on HPC clusters
11:00 – 12:30 Exercises and bring-your-own-code


Sarah Peter (LCSB, Elixir-Luxembourg)

Nikola de Lange (LCSB, Elixir-Luxembourg)


Sarah Peter Roland Krause