diff --git a/.editorconfig b/.editorconfig
index 014c2383bd..449f446a3b 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -10,3 +10,13 @@ indent_style = space
 
 [*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
+
+# ignore python and markdown files
+[*.py]
+indent_style = unset
+
+[**/{CONTRIBUTING,README}.md]
+indent_style = unset
+
+[**/Makefile]
+indent_style = unset
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 11db7939d9..01d86fad98 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -35,6 +35,8 @@ jobs:
           gh pr checkout $PR_NUMBER
 
       - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
 
       - name: Install packages
         run: |
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index dfe10b5bbb..2d16838e44 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -35,6 +35,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
+          cache: pip
 
       - name: Install python dependencies
         run: |
@@ -47,19 +48,6 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier and editorconfig-checker
-        run: npm install -g prettier editorconfig-checker
-
-      - name: Install ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-
       # Build a pipeline from the template
       - name: nf-core create
         run: |
@@ -78,15 +66,8 @@ jobs:
         working-directory: create-lint-wf
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-lint-wf/nf-core-testpipeline
-
-      - name: Run Ruff check
-        run: ruff check create-lint-wf/nf-core-testpipeline
-      - name: Run Ruff format
-        run: ruff format create-lint-wf/nf-core-testpipeline
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-lint-wf
 
       # Update modules to the latest version
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index d86a77c598..7c970d6eb8 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -51,18 +51,6 @@ jobs:
         with:
           version: latest-everything
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      # Install the editorconfig linting tools
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
       # Create template files
       - name: Create template skip all (except github)
         run: |
@@ -107,11 +95,8 @@ jobs:
         run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-test-lint-wf/my-prefix-testpipeline
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: Run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-test-lint-wf
 
       # Remove TODO statements
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 0fdc1a2d97..ec495a3f9f 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -24,29 +24,17 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      - name: Run 'prettier --write'
-        run: prettier --write ${GITHUB_WORKSPACE}
-
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
+          cache: "pip"
 
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff
-        run: |
-          ruff check --fix .
-          ruff format .
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
       - name: Commit & push changes
         run: |
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 1df7ac8fab..686cd2eb07 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -13,81 +13,9 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  EditorConfig:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      # Run editor config check only on files not covered by a linter
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
-
-  Prettier:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  Ruff:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff check
-        run: ruff check .
-
-      - name: Run Ruff format
-        run: ruff format .
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v2
-        with:
-          message: |
-            ## Python linting (`ruff`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`ruff`](https://github.com/astral-sh/ruff): `pip install ruff`
-            * Fix formatting errors in your pipeline: `ruff check --fix .` and `ruff format .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up Ruff in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
-  static-type-check:
-    runs-on: ["self-hosted"]
+  Pre-commit:
+    name: Pre-commit
+    runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -100,28 +28,5 @@ jobs:
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
-      - name: Get Python changed files
-        id: changed-py-files
-        uses: tj-actions/changed-files@v23
-        with:
-          files: |
-            *.py
-            **/*.py
-      - name: Run if any of the listed files above is changed
-        if: steps.changed-py-files.outputs.any_changed == 'true'
-        run: mypy ${{ steps.changed-py-files.outputs.all_changed_files }}
+      - name: Run pre-commit
+        run: pre-commit run --all-files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8dc52f06fe..fb2a67bace 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,11 +6,18 @@ repos:
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
       - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0" # Use the sha / tag you want to point at
+    rev: "v1.8.0"
     hooks:
       - id: mypy
         additional_dependencies:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a88a14265..2c8f522fe4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@
 
 - Rename `release-announcments.yml` to `release-announcements.yml` ([#2610](https://github.com/nf-core/tools/pull/2610))
 - Fix `nextflow.config` `docker.runOptions` ([#2607](https://github.com/nf-core/tools/pull/2607))
+- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
 
 ### General
 
diff --git a/docs/api/Makefile b/docs/api/Makefile
index f961e4ded1..ab30a5051e 100644
--- a/docs/api/Makefile
+++ b/docs/api/Makefile
@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index b6b3190776..9b990088ab 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -22,3 +22,11 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index 31e8cd2b36..d9986bd30f 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -24,32 +24,25 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: "pip"
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run pre-commit
+        run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        if: env.status == 'fail'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix linting with pre-commit"
           git push {%- endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 18531f882e..fa332827b0 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -11,73 +11,22 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  Ruff:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff check
-        run: ruff check .
-
-      - name: Run Ruff format
-        run: ruff format .
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v2
-        with:
-          message: |
-            ## Python linting (`ruff`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`ruff`](https://github.com/astral-sh/ruff): `pip install ruff`
-            * Fix formatting errors in your pipeline: `ruff check --fix .` and `ruff format .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          cache: "pip"
 
-            We highly recommend setting up Ruff in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 0c31cdb99f..984321ff26 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec