The nf-core project is a widely recognized community resource that provides a rich collection of modular, reusable workflows and developer tools, along with best practices for building high-quality bioinformatics pipelines. While these resources are highly valuable, the breadth and sophistication of nf-core can be daunting for newcomers, making it challenging to know where to start.
Hello nf-core is a hands-on tutorial designed for students and early-career researchers who have some familiarity with Nextflow and want to take the next step in workflow development. The tutorial aims to equip participants with foundational skills in three key areas: (1) understanding the structure and conventions of nf-core pipelines, (2) integrating community-curated modules, and (3) creating their own nf-core-compatible modules.
Through guided, goal-oriented exercises, participants will learn to:
- Find and run existing nf-core pipelines, exploring their directory structure and configuration systems.
- Adapt a simple Nextflow workflow into an nf-core-compatible pipeline using template scaffolds.
- Integrate pre-built nf-core modules and create new modules following community standards.
By the end of the tutorial, participants will have transformed a basic Nextflow workflow into an nf-core-style pipeline with standardized structure and reusable components, gaining practical skills to confidently leverage nf-core resources in their own bioinformatics projects. Additional study-at-home materials will be provided to continue building expertise after the course.
The training materials are open-source and freely available on the Nextflow training portal at https://training.nextflow.io/latest/hello_nf-core
About
This tutorial aims to teach participants to use and develop nf-core compatible modules and pipelines, and to utilize nf-core tooling effectively.
By the end of this training, participants will be able to:
- Find and run nf-core pipelines
- Describe the code structure and project organization of nf-core pipelines
- Create a basic nf-core compatible pipeline from a template
- Convert basic Nextflow modules to nf-core compatible modules
- Add nf-core modules to an nf-core compatible pipeline
This tutorial is designed for learners who have some familiarity with Nextflow and want to build on that foundation using nf-core. Some experience with the command line, basic scripting concepts, and workflow development is assumed. Prerequisites can be satisfied by completing the “Hello Nextflow” tutorial. Some of the exercises demonstrate the use of domain-specific bioinformatics pipelines, but the focus is on the mechanics, so specific scientific domain knowledge is not required. No prior experience with nf-core or advanced programming is assumed.
Speakers
Geraldine Van der Auwera
Lead Developer Advocate at Seqera