nf-core-lint

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              # lint current directory
nf-core pipelines lint --dir /path  # lint a specific pipeline

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

1. Run nf-core pipelines lint — note failing tests.
2. Focus: nf-core pipelines lint -k <test_name>.
3. For auto-fix: ensure clean git state first, then nf-core pipelines lint --fix.
4. Review diff before committing.
5. Re-run full lint to confirm green.

References

• Lint test documentation
• nf-core tools CLI docs