Doctoral School

UGent Nextflow Training Workshop for Beginners 2024

Target audience

Life Sciences (PhD, Postdoc) researchers (Medicine, Bio-engineering, Biomedical science, Veterinary science, Biology, Biochemistry, Biotechnology, etc) in need of efficient pipeline tooling.

Level

  • Beginner level (no knowledge of Nextflow required)
  • Basic knowledge of pipelines and bioinformatics required
  • English, basic HPC/Linux knowledge required.

Organizing and scientific committee

  • Matthias De Smet
  • dr. Tom Sante
  • Nicolas Vannieuwkerke
  • Dr. Mattias Van Heetvelde
  • Prof. dr. Elfride De Baere

Abstract

Nextflow is a workflow framework that can be used by a bioinformatician to integrate bash/python/perl/other scripts into a one cohesive pipeline that are portable, reproducible, scalable and checkpointed. This way of building analysis pipelines has become very popular, and several commercial companies have been offering (expensive) courses on the subject for years. We aim to roll-out a three-day beginner’s program at Ghent University to allow our PhDs (and postdocs) to learn this valuable skill at a low cost. This course contains all the need-to-know required to register for the requested ‘UGent Nextflow Training Workshop for Advanced Users 2023’.

Objectives

In this course the participants will learn the basics of Nextflow as well as learn the fundamental best practices of bioinformatic pipeline development. We will help them understand how workflow management systems can accelerate their research by using state-of-the-art, open-source software to make complex analyses routine. By the end of the course, they should perform a personal custom analysis by building a pipeline using Nextflow! The idea is to give them the knowledge and the tools to understand and implement the concept in their own research.

Dates and venue

5, 6 and 7 February 2024 - from 9h- 17h30

Campus UZGent 4K3 room 4.1 - Corneel Heymanslaan 10 (9000 Gent)

Preliminary programme

Day 1: Getting ready to use Nextflow

  • Environment setup
  • Introduction to Nextflow
  • Building a simple RNA-seq workflow with Nextflow
  • Dependencies and containers

Day 2: Understanding Nextflow

  • Channels: keep data moving smoothly
  • Processes: getting stuff done
  • Operators: control your channels
  • Groovy: the backbone of Nextflow
  • Modularization: (re)use building blocks

Day 3: Running Nextflow on VSC infrastructure

  • Configuration
  • Deployment on HPC
  • Cache and resume
  • Troubleshooting
  • nf-core
  • Q&A

Registration

Registration fee

Free of charge for Doctoral School members.

Number of participants

Maximum 20

Language

English

Evaluation method

100% attendance

After successful participation, the Doctoral Schools will add this course to your curriculum of the Doctoral Training Programme in Oasis. Please note that this can take up to one to two months after completion of the course.