From nf-core
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.
How this skill is triggered — by the user, by Claude, or both
Slash command
/nf-core:nf-core-lintThe summary Claude sees in its skill listing — used to decide when to auto-load this skill
Validates a pipeline against nf-core guidelines — same tests that run in CI.
Validates a pipeline against nf-core guidelines — same tests that run in CI.
nf-core modules lint is a separate command).nf-core pipelines lint # lint current directory
nf-core pipelines lint --dir /path # lint a specific pipeline
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
| 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 |
| 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 |
.nf-core.ymlDisable entire tests or exclude specific files:
lint:
actions_awsfulltest: False
pipeline_todos: False
files_exist:
- docs/images/custom_logo.png
nf-core pipelines lint — note failing tests.nf-core pipelines lint -k <test_name>.nf-core pipelines lint --fix.Guides creation, editing, and verification of skills for AI coding agents using test-driven development with subagent scenarios. Use when authoring or debugging skills.
npx claudepluginhub edmundmiller/nf-core-skills --plugin nf-core