Nextflow for reproducible and automated data analysis
16 and 17 November
General context
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.
Kristofer Davie
Bioinformatician with over 8 years of experience in the analysis of a wide variety of next generation sequencing data types, with a strong focus on the analysis of single cell data (sc/snRNA-seq, scATAC-seq, Spatial technologies).
Program
09:30 - 10:30 - Bulding 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
16 November 2023 - 17 November 2023
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
16 November 2023 - 17 November 2023
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.
16 November 2023 - 17 November 2023
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).