Nextflow for reproducible and automated data analysis
2 days
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).
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.
Practical info
Info for trainer
Elixir code: 7547