Training courses: Introduction to Nextflow for BITS2025

Course Description

The course will teach you what Nextflow is, and how to develop your own pipelines with Nextflow.

The first part of the course covers the core components of the Nextflow language and is specially targeted to newcomers. After this course, you will have learned enough detail to be able to develop simple but fully functional pipelines. It also covers key elements of pipeline design, development and configuration practices.

You will also be introduced to nf-core, a community effort to develop and maintain a curated set of analysis pipelines built using Nextflow. It provides a standardised set of best practices, guidelines, and templates for building and sharing scientific pipelines. nf-core is an open-source community which welcomes everyone to join and contribute to.

The second part of the course explores the more advanced features of the Nextflow language and runtime. You will learn how to use them to write efficient and scalable data-intensive workflows.

Important Dates

• Deadline for applications: 6th June 2025. Priority will be given to BITS2025 registered participants that will apply by 26th May 2025.
• Participants will be notified immediately for acceptance to the course, while places last
• Course date: 10-11 June 2025

Venue

University “Federico II” Naples, Facoltà di Biotecnologie. Via Tommaso De Amicis, 95, 80131 Napoli.

Fee

The course does not include a fee, but the participants are expected to pay their own travel and accommodation costs (if any).

Selection procedure

A maximum of 30 participants will be selected on a first-come - first-served basis. Selected participants will be notified immediately for acceptance to the course, while places last, and in any case no later than 6th June 2025.

Instructors

• Júlia Mir Pedrol, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
• Jose Espinosa-Carrasco, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain

Organizers and Instructors

• Anna Marabotti, University of Salerno and ELIXIR-IT Training Platform, Italy
• Margherita Mutarelli, Istituto di Scienze Applicate e Sistemi Intelligenti “Eduardo Caianiello” ISASI-CNR, Italy
• Teresa Colombo, Institute of Molecular Biology and Pathology, IBPM-CNR, ELIXIR-IT Training Platform, Italy

Contacts

For all kinds of queries, please contact the organisers Anna Marabotti at: amarabotti@unisa.it or Margherita Mutarelli at: margherita.mutarelli@isasi.cnr.it

Target Audience

The workshop is open to anyone who wants to learn about the Nextflow programming language and wants to be able to build their own Nextflow pipelines. The second day (Advanced Nextflow) is for those who have attended the first day (Hello Nextflow) or who already have a good knowledge of Nextflow and can already build basic pipelines with it.

Aims of the course

• Learn what Nextflow is
• Be able to code a basic pipeline with Nextflow
• Learn what nf-core is
• Learn the advanced features of Nextflow
• Be able to write efficient and scalable, more complex, workflows

Resources and tools covered

• Nextflow
• nf-core

Learning Outcomes

By the end of this course, the participants will be able to:

• Write their own Nextflow pipelines
• Contribute to nf-core
• Write efficient and scalable pipelines

Prerequisites

Participants are required to bring their own personal laptop.

For the first day of the course, participants are expected to:

• Have a good knowledge of how to use a terminal.
• Have a GitHub account and be able to use Codespaces (see GitHub Codespaces setup docs). [PREFERRED OPTION]
• Alternatively you can follow the instructions for local installation and use the Devcontiners extension if you prefer using VSCode.

For the second day of the course, participants are expected to:

• All of the above
• Have a good knowledge of Nextflow, or have attended the first day of the course.

Registration

Application Form

Programme