Nextflow documentation is migrating

Nextflow documentation is being migrated to docs.seqera.io/nextflow. This site will remain available throughout the migration.

Overview

Nextflow modules are reusable units of pipeline logic (i.e., processes, workflows, and functions) that you can share across projects. By packaging common tasks as modules, you avoid duplicating code and benefit from community improvements.

There are two ways to use modules in Nextflow:

Local modules

Local modules are Nextflow scripts stored directly in your project. You include definitions from local modules using the include keyword with a relative path:

include { FASTQC } from './modules/fastqc'

Local modules are well suited for project-specific logic that is not intended for reuse or sharing. See Modules for details on module inclusion syntax, aliases, templates, and binaries.

Registry modules

New in version 26.04.0.

The Nextflow module registry hosts registry modules in a centralized repository. You manage them with the nextflow module command. Registry modules follow a standard structure with metadata (meta.yml), documentation (README.md), and a module script (main.nf) for version management, integrity checking, and discoverability.

Key features of registry modules:

  • Discoverability: Search for modules by keyword or name and browse available versions.

  • Version management: Pin specific versions or use the latest release, with automatic integrity checking via checksums.

  • Direct execution: Run modules as standalone workflows for ad-hoc tasks or testing without writing a wrapper script.

  • Standard structure: Each module includes a script (main.nf), metadata (meta.yml), and documentation (README.md), enabling consistent tooling and automation.

Note

Modules from the nf-core community are automatically mirrored to the Nextflow module registry under the nf-core namespace. You can install and use them directly without any additional configuration.

Install registry modules into your project and include them by name:

$ nextflow module install nf-core/fastqc

include { FASTQC } from 'nf-core/fastqc'

For more information about registry modules, see: