.pre-commit-config.yaml

default_stages: [commit]

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v4.0.1
  hooks:
  - id: check-yaml
  - id: check-toml
  - id: fix-encoding-pragma
  - id: end-of-file-fixer
  - id: trailing-whitespace
  - id: check-added-large-files
    args: ['--maxkb=5000']
- repo: https://github.com/PyCQA/isort
  rev: 5.9.3
  hooks:
  - id: isort
- repo: https://github.com/psf/black
  rev: 21.9b0
  hooks:
  - id: black
- repo: https://github.com/pre-commit/mirrors-mypy
  rev: v0.910-1
  hooks:
  - id: mypy
    args: ['--ignore-missing-imports', '--disable-error-code', 'name-defined', '--disable-error-code', 'attr-defined']
- repo: https://github.com/PyCQA/flake8
  rev: 4.0.1
  hooks:
  - id: flake8
    entry: pflake8
    additional_dependencies:
    - flake8-annotations
    - flake8-bandit
    - flake8-bugbear
    - flake8-comprehensions
    - flake8-docstrings
    - flake8-pytest-style
    - flake8-spellcheck
    - darglint
    - pyproject-flake8
- repo: https://github.com/snakemake/snakefmt
  rev: 0.4.4
  hooks:
    - id: snakefmt
- repo: local
  hooks:
    - id: snakelint
      name: snakelint
      language: system
      files: 'workflow/Snakefile'
      pass_filenames: false
      entry: snakemake --lint
- repo: https://github.com/lorenzwalthert/precommit
  rev: v0.1.3.9133
  hooks:
    - id: style-files
    - id: parsable-R
    - id: lintr
      verbose: true