Merge branch 'dev' into dev

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

@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -27,14 +27,14 @@ jobs:
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -48,7 +48,9 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier

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

@@ -33,13 +33,13 @@ jobs:
           - "template_skip_nf_core_configs.yml"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -52,7 +52,9 @@ jobs:
           version: latest-everything
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier

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

@@ -26,13 +26,13 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,9 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -38,10 +40,10 @@ jobs:
           # Override to remove the default --check flag so that we make changes
           options: "--color"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: python-isort
         uses: isort/isort-action@v1.0.0
         with:

.github/workflows/lint-code.yml

@@ -14,11 +14,13 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -28,11 +30,13 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -41,9 +45,9 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,29 +75,50 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: python-isort
         uses: isort/isort-action@v1.1.0
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"
 
   static-type-check:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
-      - run: pip install mypy types-PyYAML
+          python-version: 3.12
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          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

.github/workflows/push_dockerhub_dev.yml

@@ -13,7 +13,7 @@ concurrency:
 jobs:
   push_dockerhub:
     name: Push new Docker image to Docker Hub (dev)
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

.github/workflows/push_dockerhub_release.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest

.github/workflows/pytest.yml

@@ -24,37 +24,63 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
-  pytest:
-    runs-on: ${{ matrix.runner }}
+  setup:
+    runs-on: ["ubuntu-latest"]
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
           - runner: "ubuntu-20.04"
             python-version: "3.8"
 
     steps:
-      - uses: actions/checkout@v3
-        name: Check out source-code repository
+      - name: Check conditions
+        id: conditions
+        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
+
+      - name: Check out source-code repository
+        uses: actions/checkout@v4
+        if: ${{ env.run-tests == 'true' }}
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
+        if: ${{ env.run-tests == 'true' }}
+    outputs:
+      python-version: ${{ matrix.python-version }}
+      runner: ${{ matrix.runner }}
+      run-tests: ${{ env.run-tests }}
+
+  test:
+    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
+    needs: setup
+    if: ${{ needs.setup.outputs.run-tests == 'true' }}
+    runs-on: ${{ needs.setup.outputs.runner }}
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Set up Python ${{ needs.setup.outputs.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ needs.setup.outputs.python-version }}
+          cache: "pip"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
       - name: Downgrade git to the Ubuntu official repository's version
-        if: ${{ matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8' }}
+        if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
         run: |
           sudo apt update
-          sudo apt remove git git-man
+          sudo apt remove -y git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
-          sudo apt install git
+          sudo apt install -y git
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
@@ -64,6 +90,21 @@ jobs:
         with:
           version: "latest-everything"
 
+      - 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: Test with pytest
         run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
 

.github/workflows/rich-codex.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:

.github/workflows/sync.yml

@@ -36,10 +36,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -48,10 +48,10 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |