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 for bioinformatics analysis, together with the growing demand for efficient and reproducible workflows, has created opportunities to adopt new tools that optimize pipeline execution.

Nextflow is a powerful workflow orchestrator that addresses these needs through its native capabilities. It enables software to run independently and in parallel, supports integration with other modules and pipelines, and allows workflows to scale across different computing environments.

This course will provide participants with hands-on experience in wrapping pipelines with Nextflow, streamlining analyses, and creating modular, plug-and-play workflows. Participants will also learn how to take advantage of Nextflow features such as different software-management technologies and executors, ranging from local environments to high-performance computing clusters.

Audience

This course is designed for PhD students, postdoctoral researchers, and other life-science researchers from academia and industry who want to automate their analyses and improve the scalability and reproducibility of their pipelines using a workflow manager.

Learning Outcomes

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

• Recognize the benefits of using a workflow orchestrator for routine analyses.
• Develop their own pipelines using Nextflow.
• Modularize pipelines to improve execution control.
• Run pipelines in different computing environments.

Required Knowledge and Competencies

Participants should be familiar with UNIX and Bash scripting. Prior completion of the SIB courses First Steps with UNIX in Life Sciences and UNIX Fundamentals is recommended.

Technical Requirements

Participants must bring their own laptop. They must also create or use a GitHub account and sign in to GitHub Codespaces during the course.

SIB course webpage

Day 1 (13:00–17:00)

• Lecture: Workflow managers and Nextflow architecture.
• Hands-on session: Hello World pipeline.
• Lecture: Modularization and workflows.
• Hands-on session: RNA-seq pipeline.

Day 2 (13:00–17:00)

• Lecture: Executors, profiles, and software management.
• Hands-on session: Metagenomics pipeline.
• Hands-on session: Wrapping your own pipeline.
• Lecture: nf-core.
• Wrap-up and closing remarks.

online

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

Registration fees
CUSO members: Free

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 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 as well as SIB, we will not be able to cover your fees.

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