Nextflow for reproducible and automated data analysis
Nextflow for reproducible and automated data analysis
27 November 2025, 9h30- 17h00
28 November 2025, 9h30-17h00
General context
This course is part of a micro-credential track, which offers the added value of being akin to a mini-diploma. When following the full track, you will be able to improve the reproducibility of your research.
Check this opportunity: Reproducible Data Analysis: an Essential Capability in Modern Science
Are you a research staff member working with bioinformatics data? This hands-on training is designed to help you build scalable, reproducible data analysis pipelines using Nextflow. As data volumes grow and analyses become more complex, mastering workflow management tools is essential for ensuring reproducibility and efficiency. In this course, you’ll learn how to develop and run pipelines on your local machine, HPC clusters, and cloud platforms. Starting from the basics, we’ll guide you through building a simple pipeline and progressively enhance it using Nextflow’s modern DSL2 syntax. By the end, you’ll be equipped with practical skills to streamline your own analyses and collaborate more effectively across computational environments
- Describe the core components of Nextflow (e.g., channels, processes, modules, workflows) and explain their roles in pipeline development.
- Construct a basic Nextflow pipeline using DSL2 syntax and execute it on a local machine.
- Modify configuration files to adapt pipeline parameters for different computing environments (e.g., local, cluster, cloud).
- Apply best practices for reproducibility and scalability in workflow design.
- Debug and refactor a simple pipeline to improve clarity, modularity, and performance.
Bioinformaticians with no or little knowledge of containers or workflow pipelines.
Completion of an HPC course is mandatory for individuals without prior experience in High Performance Computing before enrolling
You're familiar with doing bioinformatics on the command line and with Docker.
- If you have no experience with the command line, we strongly recommend following the Linux initiation training first.
If you have no experience with Docker, you can follow our Docker training.
Trainers
Kobe Lavaerts
Bioinformatician at VIB Nucleomics Core in Leuven. Currently mainly focusing on operating and developing routine pipelines for processing raw sequencing data.
Nicolas Vannieuwkerke
Nicolas Vannieuwkerke is a bioinformatician at CMGG (UZ Ghent) who mainly focuses on developing and maintaining Nextflow pipelines for the diagnostic NGS analyses. He is a very active member of the Nextflow community as a Nextflow ambassador and is part of the nf-core core team. Nf-core is the largest Nextflow community that creates and maintains a number of best-practice pipelines and developer resources.
Program
Building Blocks
Coffee break (provided)
Processes and Workflows
Lunch (provided)
Creating our first pipeline
Coffee break (provided)
Modules and Subworkflow
Config files, Containers and Reports
Coffee break (provided)
Exercise
Lunch (provided)
Project Challenge
Coffee break (provided)
Project Challenge
Practical info
27 November 2025 - 28 November 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
27 November 2025 - 28 November 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
27 November 2025 - 28 November 2025
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
27 November 2025 - 28 November 2025
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.