About the course

This slow-paced hands-on internal course is designed for absolute beginners who want to start using Nextflow DSL2 to achieve reproducibility of the data analysis.

Main instructors:

Luca Cozzuto

Toni Hermoso

Emilio Palumbo

Luca Cozzuto

Toni Hermoso Pulido

Emilio Palumbo

Jose Espinosa

Cris Tuni

Julia Ponomarenko

Jose Espinosa

Cris Tuni

Julia Ponomarenko

Dates, time, location

  • Dates: From 22nd to 25th of April 2025.

  • Location: CRG training room

Outline

This Nextflow course will train participants to build Nextflow pipelines and run them with Linux containers.

Learning objectives

  • Execute/Run a Nextflow pipeline.

  • Describe and explain Nextflow basic concepts.

  • Test and modify a Nextflow pipeline.

  • Implement short blocks of code into a Nextflow pipeline.

  • Use containers in Nextflow processes

  • Develop a Nextflow pipeline from scratch.

  • Run a pipeline in diverse computational environments (local, HPC, cloud).

  • Share a pipeline.

Prerequisite / technical requirements

Being comfortable working with the CLI (command-line interface) in a Linux-based environment. Knowledge of containers is not mandatory. The course materials is online in the dedicated GitHub page for self-learning.

Having a GitHub account is recommended.