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Merged
renovate merged 3 commits into from
Oct 9, 2025
Merged

Update dependency python to 3.14 #3817

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a237512
Update dependency python to 3.14
renovate[bot] Oct 8, 2025
af8bf82
[automated] Update CHANGELOG.md
nf-core-bot Oct 8, 2025
c4eb9ec
bump max python version to 3.14
mashehu Oct 8, 2025
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4 changes: 2 additions & 2 deletions .devcontainer/build-devcontainer/Dockerfile
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Expand Up @@ -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 && \
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2 changes: 1 addition & 1 deletion .devcontainer/build-devcontainer/devcontainer.json
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@@ -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",
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -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)_
6 changes: 3 additions & 3 deletions .github/workflows/changelog.yml
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Expand Up @@ -38,7 +38,7 @@ jobs:

- uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"

- name: Install packages
run: |
Expand Down Expand Up @@ -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
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4 changes: 2 additions & 2 deletions .github/workflows/create-lint-wf.yml
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions .github/workflows/create-test-lint-wf-template.yml
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Expand Up @@ -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: |
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4 changes: 2 additions & 2 deletions .github/workflows/create-test-wf.yml
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Expand Up @@ -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: |
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4 changes: 2 additions & 2 deletions .github/workflows/deploy-pypi.yml
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Expand Up @@ -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: |
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2 changes: 1 addition & 1 deletion .github/workflows/fix-linting.yml
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions .github/workflows/lint-code.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/nextflow-source-test.yml
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Expand Up @@ -28,7 +28,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"
cache: pip
cache-dependency-path: nf-core-tools/pyproject.toml

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6 changes: 3 additions & 3 deletions .github/workflows/pytest.yml
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Expand Up @@ -34,7 +34,7 @@ jobs:
runs-on: "ubuntu-latest"
strategy:
matrix:
python-version: ["3.9", "3.13"]
python-version: ["3.9", "3.14"]
runner: ["ubuntu-latest"]

steps:
Expand Down Expand Up @@ -154,10 +154,10 @@ jobs:
- runner=2cpu-linux-x64
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 coverage
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4 changes: 2 additions & 2 deletions .github/workflows/sync.yml
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Expand Up @@ -72,10 +72,10 @@ jobs:
path: nf-core/${{ matrix.pipeline }}
fetch-depth: "0"

- 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: |
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2 changes: 1 addition & 1 deletion .github/workflows/update-template-snapshots.yml
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Expand Up @@ -63,7 +63,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"
cache: "pip"

- name: Install dependencies
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2 changes: 1 addition & 1 deletion .github/workflows/update-textual-snapshots.yml
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Expand Up @@ -36,7 +36,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"
cache: "pip"

- name: Install dependencies
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -72,6 +72,7 @@
- Update GitHub Actions ([#3795](https://github.com/nf-core/tools/pull/3795))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.13.3 ([#3791](https://github.com/nf-core/tools/pull/3791))
- Update pre-commit hook pre-commit/pre-commit-hooks to v6 ([#3797](https://github.com/nf-core/tools/pull/3797))
- Update dependency python to 3.14 ([#3817](https://github.com/nf-core/tools/pull/3817))

## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -35,7 +35,7 @@ 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=3.13 nf-core nextflow
conda create --name nf-core python=3.14 nf-core nextflow
conda activate nf-core
```

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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/.github/actions/nf-test/action.yml
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Expand Up @@ -27,7 +27,7 @@ runs:
- name: Set up Python
uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"

- name: Install nf-test
uses: nf-core/setup-nf-test@v1
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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/.github/workflows/download_pipeline.yml
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Expand Up @@ -46,7 +46,7 @@ jobs:

- uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"
architecture: "x64"

- name: Setup Apptainer
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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/.github/workflows/fix_linting.yml
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Expand Up @@ -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
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6 changes: 3 additions & 3 deletions nf_core/pipeline-template/.github/workflows/linting.yml
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Expand Up @@ -13,10 +13,10 @@ 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"

- name: Install pre-commit
run: pip install pre-commit
Expand All @@ -35,7 +35,7 @@ jobs:

- uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
with:
python-version: "3.13"
python-version: "3.14"
architecture: "x64"

- name: read .nf-core.yml
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2 changes: 1 addition & 1 deletion tests/test_cli.py
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Expand Up @@ -169,7 +169,7 @@ def test_cli_download(self, mock_dl):
"force": None,
"platform": None,
"download-configuration": "yes",
"tag": "3.13=testing",
"tag": "3.14=testing",
"container-system": "singularity",
"container-library": "quay.io",
"container-cache-utilisation": "copy",
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