Nextflow in Action: Build Smarter, Faster, Reproducible Pipelines (SIB)

Nov 18-19, 2026

Dr Valeria Di Cola, Training Manager (SIB)

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.

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.

SIB course webpage 

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.

online

4 spots: CUSO EE
4 spots: CUSO Microbiology
2 spots: CUSO StarOmics

Registration fees
CUSO members: Free
Others: contact ecologie-evolution(a)cuso.ch

Cancellation Policy
In case of cancellations, before the 1st deadline (04.11.2026): free
Late cancellations (after 04.11.2026) or no-show: 50 CHF administrative fee

Important for CUSO Ecology&Evolution, CUSO StarOmics, CUSO 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.

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