Merge branch 'dev' of github.com:nf-core/tools into use-pre-commit-fo…

…r-linting-jobs

# Conflicts:
#	.github/workflows/lint-code.yml

.github/workflows/create-lint-wf.yml

@@ -32,7 +32,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: pip

.github/workflows/create-test-lint-wf-template.yml

@@ -37,7 +37,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/create-test-wf.yml

@@ -30,7 +30,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/deploy-pypi.yml

@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/fix-linting.yml

@@ -25,7 +25,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: "pip"

.github/workflows/lint-code.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: "pip"

.github/workflows/pytest.yml

@@ -54,7 +54,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"

.github/workflows/rich-codex.yml

@@ -8,7 +8,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.x
           cache: pip

.github/workflows/sync.yml

@@ -49,7 +49,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/tools-api-docs-dev.yml

@@ -27,7 +27,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/tools-api-docs-release.yml

@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -37,7 +37,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           architecture: "x64"

nf_core/pipeline-template/.github/workflows/release-announcements.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies