Chapter 1: Introduction

An nf-core module is an atomic, standardised, reproducible, and tested Nextflow DSL2 module. You can install an nf-core module into any Nextflow pipeline with a single command, then integrate it into your workflow thanks to its consistent internal structure.

Why use nf-core modules

• Efficiency: reuse community modules instead of writing your own.
• Consistency: every module follows the same structure, so modules connect together predictably.
• Documentation: each module ships with metadata and descriptions.
• Future-proofing: modules cover all inputs and outputs from the start, so you avoid rewrites when requirements change.
• Automation: standardisation enables future automated workflow development.

Scope

This training covers:

• Writing nf-core modules.
• Using nf-core modules in official nf-core pipelines and custom Nextflow pipelines.

Learning objectives

By the end of this training, you will be able to:

• Identify the file components of an nf-core module.
• Apply the nf-core module specifications.
• Locate documentation for developing an nf-core module.
• Write an nf-core module.
• Write nf-test unit tests for an nf-core module.
• Follow the workflow for contributing modules to the community repository.
• Use an nf-core module in any Nextflow pipeline.

Chapters

• Chapter 1: Introduction
• Chapter 2: Getting started
• Chapter 3: What is an nf-core module?
• Chapter 4: Generating boilerplate files
• Chapter 5: Writing an nf-core module
• Chapter 6: Testing an nf-core module
• Chapter 7: Development workflow
• Chapter 8: Using nf-core modules in pipelines