| name | nf-core-lint |
| description | Run and interpret `nf-core pipelines lint` to validate a Nextflow pipeline against nf-core community guidelines. Use when the user wants to check pipeline compliance, fix lint failures, run specific lint tests, or configure `.nf-core.yml` lint overrides. |
| license | MIT |
| metadata | {"author":"nf-core","version":"0.1.0"} |
nf-core pipelines lint
Validates a pipeline against nf-core guidelines — same tests that run in CI.
When to use
- User asks to lint, validate, or check an nf-core pipeline.
- CI lint checks are failing and the user needs to diagnose or fix them.
- User wants to disable or configure specific lint tests.
When not to use
- Generic Nextflow scripts outside an nf-core pipeline.
- Module-level linting (
nf-core modules lint is a separate command).
Basic usage
nf-core pipelines lint
nf-core pipelines lint --dir /path
Targeted runs
Use -k to iterate on a single failing test:
nf-core pipelines lint -k files_exist
nf-core pipelines lint -k files_exist -k files_unchanged
Key flags
| Flag | Purpose |
|---|
--dir <path> | Target directory (default: .) |
-k / --key <test> | Run only named test(s), repeatable |
--show-passed | Show passing tests in output |
--fix | Auto-fix issues (requires clean git working tree) |
--json <file> | Write results as JSON |
--markdown <file> | Write results as Markdown |
Interpreting results
| Status | Meaning |
|---|
| FAILED | Must fix — blocks nf-core listing |
| WARNED | Best-practice issue, not blocking |
| PASSED | Shown only with --show-passed |
| IGNORED | Disabled in .nf-core.yml |
Configuration via .nf-core.yml
Disable entire tests or exclude specific files:
lint:
actions_awsfulltest: False
pipeline_todos: False
files_exist:
- docs/images/custom_logo.png
Fix workflow
- Run
nf-core pipelines lint — note failing tests.
- Focus:
nf-core pipelines lint -k <test_name>.
- For auto-fix: ensure clean git state first, then
nf-core pipelines lint --fix.
- Review diff before committing.
- Re-run full lint to confirm green.
References
