Merge branch 'dev' into pin-plugin-version

.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 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
 
  - name: Install python dependencies
  run: |

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

@@ -36,10 +36,10 @@ jobs:
  - uses: actions/checkout@v4
  name: Check out source-code repository
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
 
  - name: Install python dependencies
  run: |

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

@@ -29,10 +29,10 @@ jobs:
  - uses: actions/checkout@v4
  name: Check out source-code repository
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
 
  - name: Install python dependencies
  run: |

.github/workflows/deploy-pypi.yml

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

.github/workflows/fix-linting.yml

@@ -40,10 +40,10 @@ jobs:
  # Override to remove the default --check flag so that we make changes
  options: "--color"
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
  - name: python-isort
  uses: isort/isort-action@v1.0.0
  with:

.github/workflows/lint-code.yml

@@ -80,10 +80,10 @@ jobs:
  - name: Check out source-code repository
  uses: actions/checkout@v4
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
  - name: python-isort
  uses: isort/isort-action@v1.1.0
  with:
@@ -96,7 +96,7 @@ jobs:
  - uses: actions/checkout@v4
  - uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
  cache: "pip"
 
  - name: Install dependencies

.github/workflows/pytest.yml

@@ -28,7 +28,7 @@ jobs:
  runs-on: ["ubuntu-latest"]
  strategy:
  matrix:
- python-version: ["3.8", "3.12"]
+ python-version: ["3.8", "3.11"]
  runner: ["ubuntu-latest"]
  include:
  - python-version: "3.8"

.github/workflows/sync.yml

@@ -48,10 +48,10 @@ jobs:
  path: nf-core/${{ matrix.pipeline }}
  fetch-depth: "0"
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ 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@v4
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ 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@v4
 
- - name: Set up Python 3.12
+ - name: Set up Python 3.11
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.11
 
  - name: Install python dependencies
  run: |

CHANGELOG.md

@@ -47,7 +47,6 @@
 - Update `schema build` functionality to automatically update defaults which have changed in the `nextflow.config`([#2479](https://github.com/nf-core/tools/pull/2479))
 - Change testing framework for modules and subworkflows from pytest to nf-test ([#2490](https://github.com/nf-core/tools/pull/2490))
 - `bump_version` keeps now the indentation level of the updated version entries ([#2514](https://github.com/nf-core/tools/pull/2514))
-- Run tests with Python 3.12 ([#2522](https://github.com/nf-core/tools/pull/2522)).
 - Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545))
 - Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)).
 - GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)).

README.md

@@ -76,7 +76,7 @@ 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=3.12 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: "3.12"
+ python-version: "3.11"
  architecture: "x64"
 
  - name: Install dependencies