Nextflow in Action: Build Smarter, Faster, Reproducible Pipelines

18-19 November 2026

Dr. Valeria Di Cola, Training Manager (SIB)

M. Jeferyd Yepes Garcia, UNIFR & SIB

Overview
The rapid evolution of computational infrastructure to perform bioinformatics analysis and the claim for more efficient and reproducible workflows have opened a door to include new tools that optimize pipeline execution. The workflow orchestrator Nextflow has arisen as a great alternative to meet these needs given its native capabilities such as the possibility to run the software independently and in parallel, the chance to couple it to many other modules or pipelines and its scalability.
This course empowers the participants with hands-on strategies to wrap their pipelines with Nextflow, streamlining the analysis and allowing a plug-and-play modular design. In addition, the participants will learn to take advantage
from other Nextflow features such as the possibility of choosing the software management technology or using different executors from local environments until High Performance Clusters.

Audience
This course is designed for PhD students, postdoctoral and other researchers in the life sciences from both academia and industry who aim at automatizing their analyses and/or in the quest to guarantee scalability and reproducibility of their pipelines through a workflow manager.

Learning outcomes
At the end of the course, the participants are expected to:
-Recognize the benefits of wrapping their routine analysis with a workflow orchestrator.
-Develop their own pipelines wrapped with Nextflow.
-Modularize their pipelines to enhance the control execution.
-Run their pipelines in different environments.

Prerequisites
Knowledge / competencies
This course is intend to those who are familiar with UNIX and Bash scripting. Participants who have already followed the SIB courses "First Steps with UNIX in Life Sciences" and "UNIX Fundamentals".

Technical
You are required to bring your own laptop and they will be asked to sign-up/log-in on GitHub to use GitHub Codespaces.

Schedule

Day 1 13:00 -17:00
Lecture: Workflow managers and Nextflow architecture.
Hands-on: Hello world pipeline.
Lecture: Modularization and workflow.
Hands-on: RNA-seq pipeline.

Day 2 13:00 -17:00
Lecture: Executors, profiles and software management.
Hands-on: Metagenomics pipeline.
Hands-on: wrapping your pipeline.
Lecture: nf-core.
Wrapping-up and closing remarks.

SIB course webpage

online

2 spots: CUSO StarOmics

4 spots: CUSO EE

4 spots: CUSO Microbiology

Important for CUSO DPEE, StarOmics, Microbiology members:

Please register on the CUSO website using the orange button at the top of this page, in addition to any registration on the SIB website. We need your myCUSO registration to accurately plan our budget and report your participation to SIB for invoicing.

If you do not register via myCUSO, we will not be able to cover your fees.