Nextflow documentation is migrating

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

Overview

Nextflow scripts can include definitions (workflows, processes, and functions) from other scripts. When a script is included in this way, it is referred to as a module. Modules can be re-used within a pipeline and can be shared across projects. By packaging definitions as modules, you avoid duplicating code and benefit from community improvements.

There are two ways to use modules in Nextflow:

See Using modules to learn how to install and use modules in a project. See Developing modules to learn how to create and publish your own modules. See Nextflow module registry to learn how to use the Nextflow module registry.

Local modules

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

include { CAT } from './modules/cat'

workflow {
    data = channel.fromPath('data/*.txt')
    CAT(data)
}

The above snippet imports a process named CAT from the included module into the including script. The include source ./modules/cat refers to the script ./modules/cat.nf relative to the including script path.

Local modules are well suited for project-specific components that are not intended for sharing.

Registry modules

New in version 26.04.0.

Registry modules are sourced from the Nextflow registry or a compatible module registry. Like local modules, registry modules are stored in your project, but they are installed and managed using the nextflow module command.

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), spec (meta.yml), and documentation (README.md), providing a consistent structure for tooling and automation.

Note

Modules from the nf-core community are automatically mirrored to the Nextflow module registry under the nf-core namespace.

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

$ nextflow module install nf-core/fastqc

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