.pre-commit-config.yaml

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
        exclude: |
          (?x)(
              .github/workflows/latest-changes.jinja2
          )
      - id: check-yaml
      - id: check-added-large-files
        exclude: |
          (?x)(
              nextflow_bulk_rna
          )
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.9.4
    hooks:
      - id: ruff
        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
      - id: ruff-format
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: v2.6.2
    hooks:
      - id: prettier
  - repo: https://github.com/kynan/nbstripout
    rev: 0.3.9
    hooks:
      - id: nbstripout
        exclude: |
          (?x)(
              docs/examples/|
              docs/notes/
          )
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.14.1
    hooks:
      - id: mypy
        additional_dependencies: ["types-PyYAML"]