switch pre-commit to prek for development

.devcontainer/build-devcontainer/Dockerfile

@@ -9,9 +9,8 @@ COPY . /root/nfcore-tools/
 # install local nf-core tools version, and precommit hooks
 RUN cd /root/nfcore-tools/ && \
     conda install -y python=3.13 && \
-    pip install --no-cache-dir --upgrade pip setuptools wheel pre-commit && \
+    pip install --no-cache-dir --upgrade pip setuptools wheel && \
     pip install -r requirements.txt --no-cache-dir -e . && \
-    pre-commit install --install-hooks && \
     rm -rf /root/.cache/pip
 
 # Install nextflow and nf-test via conda and run conda clean

.devcontainer/setup.sh

@@ -12,5 +12,8 @@ nextflow self-update
 # Install specifically the version of tools from the workspace
 pip install --upgrade  -r requirements.txt -r requirements-dev.txt -e .
 
+# Install pre-commit hooks
+prek install --install-hooks
+
 # Update welcome message
 echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.github/workflows/changelog.yml

@@ -72,13 +72,8 @@ jobs:
           python-version: "3.14"
           cache: "pip"
 
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit checks
-        if: steps.file_changed.outputs.changed == 'TRUE'
-        run: |
-          pre-commit run --all-files
+      - name: Run pre-commit rules with prek
+        uses: j178/prek-action@v1
 
       - name: Commit and push changes
         if: steps.file_changed.outputs.changed == 'TRUE'

.github/workflows/fix-linting.yml

@@ -31,30 +31,25 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+      # Install and run prek
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@v1
         with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
+          extra-args: --config .pre-commit-config.yaml --all-files
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
 
       - name: Commit & push changes
         id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "[email protected]"
           git config user.name "nf-core-bot"

.github/workflows/lint-code.yml

@@ -15,21 +15,13 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  Pre-commit:
+  pre-commit:
     runs-on: ubuntu-latest
-    env:
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+      - name: Run prek
+        uses: j178/prek-action@v1
         with:
-          python-version: "3.14"
-          cache: "pip"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+          extra-args: --config .pre-commit-config.yaml --all-files

.pre-commit-config.yaml

@@ -9,6 +9,7 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        entry: prettier --experimental-cli --write --ignore-unknown --no-cache
         additional_dependencies:
           - [email protected]
   - repo: https://github.com/pre-commit/pre-commit-hooks

.prettierrc.yml

@@ -1,6 +1,6 @@
 printWidth: 120
 tabWidth: 4
 overrides:
-  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+  - files: "**/*.{md,yml,yaml,html,css,scss,js,cff}"
     options:
       tabWidth: 2

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### General
 
 - Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
+- Switch from pre-commit to prek for pre-commit hooks in development([#3899](https://github.com/nf-core/tools/pull/3899))
 
 ### Template
 

CONTRIBUTING.md

@@ -56,22 +56,24 @@ Ruff has been adopted for linting and formatting in replacement of Black, isort
 
 ### pre-commit hooks
 
-This repository comes with [pre-commit](https://pre-commit.com/) hooks for ruff and Prettier. pre-commit automatically runs checks before a commit is committed into the git history. If all checks pass, the commit is made, if files are changed by the pre-commit hooks, the user is informed and has to stage the changes and attempt the commit again.
+This repository comes with pre-commit hooks for ruff and Prettier, managed by [prek](https://github.com/j178/prek). Pre-commit hooks automatically run checks before a commit is committed into the git history. If all checks pass, the commit is made, if files are changed by the pre-commit hooks, the user is informed and has to stage the changes and attempt the commit again.
 
-You can use the pre-commit hooks if you like, but you don't have to. The CI on Github will run the same checks as the tools installed with pre-commit. If the pre-commit checks pass, then the same checks in the CI will pass, too.
+You can use the pre-commit hooks if you like, but you don't have to. The CI on Github will run the same checks as the tools installed with prek. If the pre-commit checks pass, then the same checks in the CI will pass, too.
 
 You can install the pre-commit hooks into the development environment by running the following command in the root directory of the repository.
 
 ```bash
-pre-commit install --install-hooks
+prek install --install-hooks
 ```
 
 You can also run all pre-commit hooks without making a commit:
 
 ```bash
-pre-commit run --all
+prek run --config .pre-commit-config.yaml --all-files
 ```
 
+Note: The `--config` flag is important in this repository to ensure prek uses the root configuration file and not the template configs in `nf_core/pipeline-template/`.
+
 ## API Documentation
 
 We aim to write function docstrings according to the [Google Python style-guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings). These are used to automatically generate package documentation on the nf-core website using Sphinx.

requirements-dev.txt

@@ -1,5 +1,6 @@
 mypy
 myst_parser
+prek
 pytest-cov
 pytest-datafiles
 responses