feat: Add lint-pipeline test

Author: edmundmiller

.pre-commit-hooks.yaml

@@ -16,4 +16,10 @@
   files: ^subworkflows/.*/.*/.*\.nf$
   pass_filenames: true
   # args: []
-# TODO lint-pipeline
+- id: lint-pipeline
+  name: Lint nf-core pipeline
+  description: Check pipeline code against nf-core guidelines.
+  entry: nf-core --hide-progress lint
+  language: python
+  types: [text]
+  # args: []

nf_core/pipeline-template/.pre-commit-config.yaml

@@ -14,6 +14,4 @@ repos:
   - repo: https://github.com/nf-core/tools
     rev: "2.14.1"
     hooks:
-      - id: lint-modules
-      - id: lint-subworkflows
-      # TODO lint-pipeline
+      - id: lint-pipeline