diff --git a/.pre-commit-hooks.yaml b/.pre-commit-hooks.yaml
new file mode 100644
index 0000000000..da043ce09c
--- /dev/null
+++ b/.pre-commit-hooks.yaml
@@ -0,0 +1,25 @@
+- 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/.*/.*/.*\.nf$
+  pass_filenames: true
+  # args: []
+- id: lint-subworkflows
+  name: Lint nf-core subworkflows
+  # description: This hook trims trailing whitespace.
+  entry: nf-core --hide-progress subworkflows lint
+  language: python
+  types: [text]
+  files: ^subworkflows/.*/.*/.*\.nf$
+  pass_filenames: true
+  # args: []
+- 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: []
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ec033ff1ee..47c8c669fb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -56,6 +56,7 @@
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
+- 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]
 
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 4dc0f1dcd7..bddd336c13 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/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: "2.14.1"
+    hooks:
+      - id: lint-pipeline
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0
deleted file mode 160000
index ee82f320cb..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
deleted file mode 160000
index f7fe48cf9d..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0
deleted file mode 160000
index dce3324acb..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit dce3324acbbe32f905afae8553e042f39404b37e
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0
deleted file mode 160000
index e2638dca91..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_details0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
deleted file mode 160000
index 74cda800a8..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 74cda800a86fd07e93bbf8e00e4890516e3d838d
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 b/tmp/pytest-of-gitpod/pytest-1/test_github_question0
deleted file mode 160000
index 444ebc5370..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_question0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 444ebc5370bf91ea808f5d65c5788064f0480045