Add nf-core-lint skill

skills/nf-core-lint/SKILL.md

@@ -0,0 +1,86 @@
+---
+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_tools_version: "4.0.2"
+---
+
+# nf-core pipelines lint
+
+Validates a pipeline against nf-core guidelines — same tests that run in CI. For nf-core/tools 4.x, expect checks for strict syntax, topic-version metadata, generated container config files, and `prek`-based code quality.
+
+## 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
+
+```bash
+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:
+
+```bash
+nf-core pipelines lint -k files_exist
+nf-core pipelines lint -k container_configs
+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 where supported; review the diff carefully |
+| `--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:
+
+```yaml
+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](https://nf-co.re/tools/docs/latest/pipeline_lint_tests/)
+- [nf-core tools CLI docs](https://nf-co.re/docs/nf-core-tools/cli/pipelines/lint)