Create pre-commit hooks

.pre-commit-hooks.yaml

@@ -0,0 +1,30 @@
+# TODO https://github.com/nf-core/tools/issues/3140
+# - id: lint-modules
+#   name: Lint nf-core modules
+#   # description: This hook trims trailing whitespace.
+#   entry: nf-core --hide-progress modules lint
+#   language: python
+#   types: [text]
+#   files: ^modules/[^/]+$
+#   pass_filenames: true
+# args: []
+# NOTE See https://github.com/nf-core/modules/pull/7084 for reasoning
+- id: lint-subworkflows
+  name: Lint nf-core subworkflows
+  description: Runs linting on all the subworkflows
+  entry: nf-core --hide-progress subworkflows lint -a
+  language: python
+  types: [text]
+  files: ^subworkflows/[^/]+$
+  alias: sw
+  pass_filenames: false
+  # args: []
+- id: lint-pipeline
+  name: Lint nf-core pipeline
+  description: Check pipeline code against nf-core guidelines.
+  entry: nf-core --hide-progress pipelines lint
+  language: python
+  types: [text]
+  pass_filenames: false
+  stages: [pre-push, manual]
+  # args: ["--fix"]

CHANGELOG.md

@@ -187,6 +187,7 @@
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
 - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 - Update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
+- Create pre-commit hooks ([#3141](https://github.com/nf-core/tools/pull/3141))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

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

@@ -11,3 +11,7 @@ repos:
     hooks:
       - id: editorconfig-checker
         alias: ec
+  - repo: https://github.com/nf-core/tools
+    rev: "3.1.0"
+    hooks:
+      - id: lint-pipeline