scdownstream/.pre-commit-config.yaml at dev · nf-core/scdownstream · GitHub

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repos:
  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: "v3.1.0"
    hooks:
      - id: prettier
        additional_dependencies:
          - prettier@3.9.10
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v6.0.0
    hooks:
      - id: trailing-whitespace
        args: [--markdown-linebreak-ext=md]
        exclude: |
          (?x)^(
              .*ro-crate-metadata.json$|
              modules/(?!local/).*|
              subworkflows/(?!local/).*|
              .*\.snap$
          )$
      - id: end-of-file-fixer
        exclude: |
          (?x)^(
              .*ro-crate-metadata.json$|
              modules/(?!local/).*|
              subworkflows/(?!local/).*|
              .*\.snap$
          )$
      - id: check-added-large-files
        args: [--maxkb=5000]
        exclude: |
          (?x)^(
              .*ro-crate-metadata.json$|
              .*\.snap$|
              lib/nfcore_external_java_deps.jar$|
              docs/.*\.(svg|pdf)$|
              assets/.*$
          )$
      - id: check-merge-conflict
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.15.13
    hooks:
      - id: ruff-check
        files: \.py$
        exclude: |
          (?x)^(
              modules/(?!local/).*|
              subworkflows/(?!local/).*
          )$
        args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"]
      - id: ruff-format
        files: \.py$
        exclude: |
          (?x)^(
              modules/(?!local/).*|
              subworkflows/(?!local/).*
          )$
  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
    rev: v0.3.0
    hooks:
      - id: nextflow-lint
        files: '\.nf$|nextflow\.config$'
        args: ["-output", "json"]
  - repo: local
    hooks:
      - id: h5ad-gzip
        name: Require gzip compression in H5AD write calls
        entry: '(?m)^(?![^\n]*compression\s*=\s*["\x27]gzip["\x27])[^\n]*(?:write_h5ad\(|\.write\([^\n]*\.h5ad)'
        language: pygrep
        files: '^(modules/local/.*/templates/.*\.(py|R)|bin/.*\.qmd)$'
      - id: block-pipeline-outdir
        name: Prevent committing output from pipeline test runs to the pipeline code itself
        entry: ./.hooks/block_pipeline_outdir.sh
        language: script