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.pre-commit-config.yaml
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.pre-commit-config.yaml
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repos:
- repo: https://github.com/pre-commit/mirrors-prettier
rev: "v3.1.0"
hooks:
- id: prettier
additional_dependencies:
- prettier@3.2.5
- repo: https://github.com/python-jsonschema/check-jsonschema
rev: 0.28.6
hooks:
- id: check-jsonschema
# match meta.ymls in one of the subdirectories of modules/nf-core
files: ^modules/nf-core/.*/meta\.yml$
args: ["--schemafile", "modules/yaml-schema.json"]
- id: check-jsonschema
# match meta.ymls in one of the subdirectories of subworkflows/nf-core
files: ^subworkflows/nf-core/.*/meta\.yml$
args: ["--schemafile", "subworkflows/yaml-schema.json"]
- id: check-github-workflows
- repo: https://github.com/renovatebot/pre-commit-hooks
rev: 37.408.2
hooks:
- id: renovate-config-validator
# use ruff for python files
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.4.10
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: local
hooks:
- id: docs_check
name: Docs check
language: system
entry: >
./docs/populate_index.sh
always_run: true
fail_fast: true
pass_filenames: false
- id: test_data_path_checks
name: Test data path checks
language: system
entry: >
./.github/check_test_data_paths.sh
always_run: true
fail_fast: true
pass_filenames: false
- id: remove_conda_defaults
name: Remove conda defaults
language: system
entry: >
find . -name environment.yml -exec sh -c "sed -i 's/ - defaults//1' {}" \;
always_run: true
pass_filenames: false
fail_fast: true