Nextflow for reproducible and automated data analysis
23 and 24 May
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 - 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
23 May 2024 - 24 May 2024
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
23 May 2024 - 24 May 2024
Leuven - Campus Gasthuisberg
Please use Parking West - Follow 'Dagcentrum Onco' to get to the O&N buildings. Take the stairs on you left after exiting Parking West. You are now in front of buidling O&N4 and on the left you find O&N5.
23 May 2024 - 24 May 2024
Leuven - Campus Gasthuisberg
Room: 404-28.05.347 (5th floor)