Run Nextflow Modules

Run modules from the Nextflow Registry natively using nextflow module commands. Everything is self-contained — no external tools or MCP needed. Modules are installed on-the-fly when run.

Modules are published under namespaces (e.g. nf-core/fastqc), and the nextflow module commands work with any of them.

Requires Nextflow 26.04 or later (for the nextflow module commands).

⛔ NEVER WRITE WRAPPER WORKFLOWS

If a module fails due to missing arguments or incorrect parameters:

❌ WRONG - Writing a wrapper workflow:

// NEVER DO THIS - even if the module fails!
include { FASTQC } from 'nf-core/fastqc'
workflow { FASTQC(Channel.fromPath('*.fq.gz')) }