Introduction to Nextflow

Duration: 4 hours / 1 days

Date: 29th of March

Time: 9:30 - 14:00 (with a 30 minutes break)

Level: Basic level with intermediate programming skills required

Format: Presential

ROOM: Dr. Aiguader 80, Barcelona. 61.212

Registration opening date: 1 of March

Deadline for registration: 15 of March

Course Description

In this course, basic concepts and characteristics of the Nextflow workflow management system will be shown. We will also explore NF-core, which is a framework of community-curated standardized analysis pipelines written in Nextflow. 

Why should you attend the course?

You will learn the basic concepts to start building your computational pipelines using a workflow management system. This will allow you to make your pipelines shareable, portable, reproducible and maintainable.  

Prerequisites

Course content and hands-ons will be easier to fully understand and fulfill if you have intermediate programming skills and basic knowledge of bash. Knowledge about containerization will also help to follow up the course. 

You should bring your own laptop with Nextflow installed. To install Nextflow version 22.10 you can follow the following documentation: 

https://www.nextflow.io/docs/latest/getstarted.html

Schedule

• Introduction to Nextflow

  • Basic concepts

  • Parameters

  • Channels

  • Processes

  • Operators

  • Modularization and DSL2

• nf-core

  • Basic concepts 

  • Pipelines

Class Pace 

We encourage the participants to do as many questions as needed during the whole course. The hands-on practical session aims to enhance dynamic learning.  

References

https://www.nextflow.io/docs/latest/index.html

https://training.seqera.io/

Short biography 

Marta Sanvicente is a PhD candidate in the Translational Synthetic Biology laboratory at Universitat Pompeu Fabra. Previously, she did the Master in Bioinformatics for Health Sciences at Universitat Pompeu Fabra (2017-2019) and Bachelor’s degree in Genetics at Universitat Autònoma de Barcelona (2013-2017). Her research interests include Next Generation Sequencing data analysis, nextflow pipelines development, and analysis, simulation and prediction of genome editing and gene writing outcomes.