tools/.pre-commit-config.yaml at main · nf-core/tools · GitHub

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repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.15.12
    hooks:
      - id: ruff-check # linter
        args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
      - id: ruff-format # formatter
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: "v3.1.0"
    hooks:
      - id: prettier
        entry: prettier --experimental-cli --write --ignore-unknown --no-cache
        additional_dependencies:
          - prettier@3.8.3
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: trailing-whitespace
        args: [--markdown-linebreak-ext=md]
        exclude: |
          (?x)^(
              .*\.snap$|
              nf_core/pipeline-template/subworkflows/.*|
              nf_core/pipeline-template/modules/.*|
              tests/pipelines/__snapshots__/.*
          )$
      - id: end-of-file-fixer
        exclude: |
          (?x)^(
              .*\.snap$|
              nf_core/pipeline-template/subworkflows/.*|
              nf_core/pipeline-template/modules/.*|
              tests/pipelines/__snapshots__/.*
          )$
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: "v1.20.2"
    hooks:
      - id: mypy
        additional_dependencies:
          - types-PyYAML
          - types-requests
          - types-jsonschema
          - types-Markdown
          - types-setuptools
          - pydantic
  - repo: https://github.com/astral-sh/uv-pre-commit
    rev: 0.11.8
    hooks:
      - id: uv-lock
  - repo: local
    hooks:
      - id: lint-test-docstrings
        name: Check lint test names are documented in docstrings
        language: system
        entry: python3 docs/api/check_lint_docstrings.py
        files: ^nf_core/(modules|subworkflows)/lint/.*\.py$