Merge branch 'dev' into update-to-python-3_10

Author: mashehu

.devcontainer/build-devcontainer/Dockerfile

@@ -5,10 +5,10 @@ FROM "mcr.microsoft.com/devcontainers/miniconda@sha256:8e262a2664fab1d53054738d3
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
 
-# Explicitly reinstall python 3.13 via conda
+# Explicitly reinstall python 3.14 via conda
 # install local nf-core tools version, and precommit hooks
 RUN cd /root/nfcore-tools/ && \
-    conda install -y python=3.13 && \
+    conda install -y python=3.14 && \
     pip install --no-cache-dir --upgrade pip setuptools wheel pre-commit && \
     pip install -r requirements.txt --no-cache-dir -e . && \
     pre-commit install --install-hooks && \

.devcontainer/build-devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 {
     "name": "nfcore-devcontainer-build",
 
-    // installs python3.13, nf-core tools from current workspace, nextflow, nf-test,
+    // installs python3.14, nf-core tools from current workspace, nextflow, nf-test,
     // and apptainer based on mcr.microsoft.com/devcontainers/miniconda image
     "build": {
         "dockerfile": "./Dockerfile",

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,4 +38,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
-        * Python version _(eg. 3.12, 3.13)_
+        * Python version _(eg. 3.13, 3.14)_

.github/workflows/changelog.yml

@@ -38,7 +38,7 @@ jobs:
 
       - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install packages
         run: |
@@ -66,10 +66,10 @@ jobs:
           echo "File changed: $file_changed"
           echo "changed=$file_changed" >> $GITHUB_OUTPUT
 
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           cache: "pip"
 
       - name: Install pre-commit

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

@@ -46,10 +46,10 @@ jobs:
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           cache: pip
 
       - name: Install python dependencies

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

@@ -58,10 +58,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install python dependencies
         run: |

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

@@ -44,10 +44,10 @@ jobs:
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         name: Check out source-code repository
 
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         name: Check out source-code repository
 
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -34,7 +34,7 @@ jobs:
       # Install and run pre-commit
       - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit

.github/workflows/lint-code.yml

@@ -22,10 +22,10 @@ jobs:
     steps:
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           cache: "pip"
 
       - name: Install pre-commit