nf-core-pipeline

nf-core pipeline

Use this skill when working inside (or scaffolding) an nf-core pipeline. nf-core pipelines are opinionated Nextflow DSL2 workflows with strict structural and style requirements enforced by nf-core lint.

When to use

• Creating a new pipeline (nf-core pipelines create).
• Adding a workflow, subworkflow, or process to an existing pipeline.
• Editing nextflow.config, nextflow_schema.json, conf/*.config, or assets/schema_input.json.
• Resolving nf-core lint failures.
• Bumping pipeline version, updating CHANGELOG.md, or preparing a release.

Do not use this skill for generic Nextflow scripts that are not part of an nf-core pipeline — use a plain Nextflow skill instead.

Core conventions

• DSL2 only. All processes are modules; the top-level main.nf only includes workflows.
• Modules live under modules/nf-core/<tool>/<subtool>/main.nf and are managed via nf-core modules install. Do not edit them in place — patch via nf-core modules patch.
• Local code goes under modules/local/, subworkflows/local/, or workflows/.
• Parameters must be declared in nextflow.config and nextflow_schema.json — they must agree.
• Tests use nf-test. Every workflow, subworkflow, and local module needs a *.nf.test file with a snapshot.

Workflow

1. Run nf-core lint early and often — it is the source of truth.
2. For new modules, prefer nf-core modules create over hand-rolling.
3. After any parameter change, run nf-core schema build to keep nextflow_schema.json in sync.
4. Update CHANGELOG.md under the ## [Unreleased] heading for every user-visible change.

Useful commands

nf-core pipelines create            # scaffold a new pipeline
nf-core pipelines lint              # run all lint checks
nf-core modules list remote         # browse available shared modules
nf-core modules install <tool>      # add a shared module
nf-core schema build                # sync nextflow_schema.json
nf-test test --profile docker       # run pipeline tests

References

• nf-core contributing guidelines
• Nextflow DSL2 docs
• nf-test docs