Only test min + max supported Python versions

Bump Python 3.8 -> 3.11 for most CI tasks, plus docker base image.

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

@@ -31,10 +31,10 @@ jobs:
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

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

@@ -35,10 +35,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

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

@@ -29,10 +29,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -38,10 +38,10 @@ jobs:
           # Override to remove the default --check flag so that we make changes
           options: "--color"
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: python-isort
         uses: isort/isort-action@v1.0.0
         with:

.github/workflows/lint-code.yml

@@ -76,10 +76,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: python-isort
         uses: isort/isort-action@v1.1.0
         with:

.github/workflows/pytest.yml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ${{ matrix.runner }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.11"]
         runner: ["ubuntu-latest"]
         include:
           - runner: "ubuntu-20.04"

.github/workflows/sync.yml

@@ -48,10 +48,10 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

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

@@ -26,10 +26,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

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

@@ -21,10 +21,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.8
+      - name: Set up Python 11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install python dependencies
         run: |

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8.9-slim
+FROM python:3.11.5-slim
 LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for the nfcore tools"
 

README.md

@@ -78,7 +78,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.8 nf-core nextflow
+conda create --name nf-core python=3.11 nf-core nextflow
 conda activate nf-core
 ```
 

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

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies