.pre-commit-config.yaml

exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/'
repos:
  - repo: https://github.com/snakemake/snakefmt
    rev: v0.10.2
    hooks:
      - id: snakefmt
        language_version: python3.11
  - repo: https://github.com/rhysd/actionlint
    rev: v1.7.4
    hooks:
      - id: actionlint
        entry: env SHELLCHECK_OPTS='--exclude=SC2027' actionlint
  - repo: https://github.com/codespell-project/codespell
    rev: v2.3.0
    hooks:
      - id: codespell
        additional_dependencies:
          - tomli
  - repo: https://github.com/google/yamlfmt
    rev: v0.14.0
    hooks:
      - id: yamlfmt
  - repo: https://github.com/pappasam/toml-sort
    rev: v0.23.1
    hooks:
      - id: toml-sort-fix
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v5.0.0
    hooks:
      - id: trailing-whitespace
      - id: check-ast
      - id: check-case-conflict
      - id: check-docstring-first
      - id: check-json
      - id: check-executables-have-shebangs
      - id: check-merge-conflict
      - id: check-shebang-scripts-are-executable
      - id: check-symlinks
      - id: check-toml
      - id: check-yaml
      - id: destroyed-symlinks
      - id: detect-private-key
      - id: end-of-file-fixer
      - id: fix-byte-order-marker
  - repo: https://github.com/pre-commit/sync-pre-commit-deps
    rev: v0.0.1
    hooks:
      - id: sync-pre-commit-deps
  - repo: https://github.com/shellcheck-py/shellcheck-py
    rev: v0.10.0.1
    hooks:
      - id: shellcheck