Nextflow for reproducible and automated data analysis
Nextflow for reproducible and automated data analysis
28 April 2025, 9h30-17h00
29 April 2025, 9h30-17h00
General context
This course is part of a micro-credential track, a micro-credential has the added value of being like a mini-diploma. When following the full track you will become able to improve the reproducibility of your research. Check this opportunity : Reproducible Data Analysis: an Essential Capability in Modern Science.
You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language.
- Understand Nextflow's basic concepts: channels, processes, modules, workflows, etc.
- Write and run a Nextflow pipeline
- Write and modify config files for storing parameters related to computing hardware as well as pipeline dependent parameters
Bioinformaticians with no or little knowledge of containers or workflow pipelines.
You're familiar with doing bioinformatics on the command-line and with Docker.
- If you have no experience with command line we strongly recommend to follow the Linux initiation training first.
- If you have no experience with Docker you can follow the 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
09:30 - 10:30 - Building Blocks
10:30 - 10:45 - Break
10:45 - 12:00 - Processes and Workflows
12:00 - 13:00 - Lunch
13:00 - 14:45 - Creating our first pipeline
14:45 - 15:00 - Break
15:00 - 17:30 - Modules and Subworkflow
09:30 - 10:45 - Config files, Containers and Reports
10:45 - 11:00 - Break
11:00 - 12:30 - Exercise
12:30 - 13:30 - Lunch
13:45 - 15:00 - Project Challenge
15:00 - 15:15 - Break
15:15 - 17:00 - Project Challenge
Practical info
28 April 2025 - 29 April 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
28 April 2025 - 29 April 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.
28 April 2025 - 29 April 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.
28 April 2025 - 29 April 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.
28 April 2025 - 29 April 2025
Ghent - VIB/UGent FSVM II
FSVM II, room L4 on the 4th floor