Nextflow for reproducible and automated data analysis
Nextflow for reproducible and automated data analysis
3 June 2027, 9h30- 17h00
4 June 202, 9h30-17h00
General context
This hands-on course introduces the principles and practice of building scalable and reproducible data analysis pipelines using Nextflow. As bioinformatics data volumes increase and analyses become more complex, workflow management tools play a key role in ensuring reproducibility and efficiency.
During the training, you will learn to develop and run pipelines on local machines, HPC clusters, and cloud platforms. Starting with the basics, the course guides you through creating a simple pipeline and enhancing it with Nextflow’s modern DSL2 syntax.
- Describe the core components of Nextflow (e.g., channels, processes, modules, workflows)
- Explain the roles of each component in pipeline development and the reproducibility aspect
- 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.
The training combines theoretical sessions with hands-on activities. In the end, a small challenge invites you to apply all the skills you have learned.
Check out this opportunity: Reproducible Data Analysis: an essential capability in modern science.
Researchers 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 containers.
- If you have no experience with the command line, we strongly recommend following the Linux initiation training first or the self-paced e-learning.
- If you have no experience with Docker, you can follow our training "Containerize data analysis with Docker & Apptainer".
This course is part of the learning path Reproducible data analysis.
Trainers
Bruna Piereck
Bruna Piereck is a bioinformatics trainer at VIB and ELIXIR-BE training coordinator deputy. She obtained a Master and PhD degree in Molecular Genetics, with a focus on Bioinformatics from the Federal University of Pernambuco, Brazil, in 2019. During her PhD, she had the chance to collaborate with the university of Luxembourg and the McGill university in Quebec Canada for a short time. Ever since she has been involved with teaching and research and Since March 2022, she joined VIB with the mission of teaching and assist other trainers in a variety of topics.
Maria Tsontaki
Maria Tsontaki is a Project Manager at the VIB Data Core. Previously working as a Bioinformatics Scientist in biotech, she is now part of the Data Core Compute team, ensuring researchers have access to computational resources and advanced software tools for scalable, reproducible data analysis. Her tasks in the team range from identifying and coordinating user needs and requests to providing bioinformatics-related support.
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
03 June 2027 - 04 June 2027
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
03 June 2027 - 04 June 2027
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
03 June 2027 - 04 June 2027
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
03 June 2027 - 04 June 2027
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.