run-module
Installation
SKILL.md
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). Workflow modules require Nextflow 26.10 or later.
Process modules vs workflow modules
A module has a kind, reported as Kind: by nextflow module search and nextflow module view:
| Kind | What it is | Example |
|---|---|---|
Process |
A single process wrapping one tool | nf-core/star/align |
Workflow |
A named workflow (subworkflow) that chains several modules; its dependencies are installed with it | nf-core/fastq_align_star (STAR + samtools sort/index/stats) |
Both kinds are searched, viewed, run, and included the same way. The differences are covered in Finding Workflow Modules and Running Workflow Modules.