.pre-commit-config.yaml

repos:
  - repo: local
    hooks:
      - id: conda-env-sorter
        name: Sort dependencies in conda environment files.
        entry: ./.github/scripts/conda_env_sorter.py
        language: python
        files: environment
        types: [yaml]
        additional_dependencies: ["ruamel.yaml"]
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: "v3.1.0"
    hooks:
      - id: prettier
        additional_dependencies:
          - prettier@3.3.3
  - repo: https://github.com/python-jsonschema/check-jsonschema
    rev: 0.29.4
    hooks:
      - id: check-jsonschema
        name: "Match meta.ymls in one of the subdirectories of modules/nf-core"
        files: ^modules/nf-core/.*/meta\.yml$
        types: [yaml]
        args: ["--schemafile", "modules/yaml-schema.json"]
      - id: check-jsonschema
        name: "Validate environment.ymls against schema"
        files: ^modules/nf-core/.*/environment\.yml$
        types: [yaml]
        args: ["--schemafile", "modules/environment-schema.json"]
      - id: check-jsonschema
        name: "Match meta.ymls in one of the subdirectories of subworkflows/nf-core"
        files: ^subworkflows/nf-core/.*/meta\.yml$
        types: [yaml]
        args: ["--schemafile", "subworkflows/yaml-schema.json"]
      - id: check-github-workflows
      - id: check-github-actions
  # use ruff for python files
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.7.3
    hooks:
      - id: ruff
        files: \.py$
        args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
      - id: ruff-format # formatter
  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
    rev: "3.0.3"
    hooks:
      - id: editorconfig-checker
        alias: ec
  - repo: https://github.com/nf-core/tools
    rev: pre-commit
    hooks:
      - id: lint-subworkflows