Template: Update python to 3.12

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -37,5 +37,5 @@ body:
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
-        * Python version _(eg. 3.10, 3.11)_
+        * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
+        * Python version _(eg. 3.11, 3.12)_

.github/workflows/changelog.yml

@@ -36,7 +36,7 @@ jobs:
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install packages
         run: |
@@ -62,10 +62,10 @@ jobs:
           git diff --exit-code ${GITHUB_WORKSPACE}/CHANGELOG.md || echo "changed=YES" >> $GITHUB_ENV
           echo "File changed: ${{ env.changed }}"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit

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

@@ -49,10 +49,10 @@ jobs:
         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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: pip
 
       - name: Install python dependencies

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

@@ -61,10 +61,10 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

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

@@ -48,10 +48,10 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -34,7 +34,7 @@ jobs:
       # Install and run pre-commit
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

.github/workflows/lint-code.yml

@@ -20,10 +20,10 @@ jobs:
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit

.github/workflows/pytest.yml

@@ -38,7 +38,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
           - python-version: "3.8"
@@ -173,12 +173,12 @@ jobs:
           cd pytest
 
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install dependencies

.github/workflows/sync.yml

@@ -56,10 +56,10 @@ 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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Template
 
 - Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([#2795](https://github.com/nf-core/tools/pull/2795))
+- Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805))
 
 ### Linting
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11-slim@sha256:ce81dc539f0aedc9114cae640f8352fad83d37461c24a3615b01f081d0c0583a
+FROM python:3.12-slim
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for the nfcore tools"
 

README.md

@@ -82,7 +82,7 @@ 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=3.11 nf-core nextflow
+conda create --name nf-core python=3.12 nf-core nextflow
 conda activate nf-core
 ```
 

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

@@ -32,7 +32,7 @@ jobs:
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:

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

@@ -34,7 +34,7 @@ jobs:
       # Install and run pre-commit
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

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

@@ -16,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit
@@ -39,7 +39,7 @@ jobs:
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies