afquery/mkdocs.yml at master · babelomics/afquery · GitHub

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site_name: AFQuery
site_description: Fast, file-based genomic allele frequency queries for large cohorts
site_url: https://babelomics.github.io/afquery/
repo_url: https://github.com/babelomics/afquery
repo_name: afquery
edit_uri: edit/master/docs/

extra_css:
  - stylesheets/extra.css

theme:
  name: material
  palette:
    - scheme: default
      primary: teal
      accent: cyan
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: teal
      accent: cyan
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.top
    - navigation.instant
    - navigation.indexes
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.code.annotate
    - toc.integrate

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.tabbed:
      alternate_style: true
  - tables
  - attr_list

extra:
  version:
    provider: mike

plugins:
  - search
  - autorefs
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            docstring_style: google
  - print-site:
      add_to_navigation: true
      print_page_title: 'AFQuery — Complete Documentation'
      add_print_site_banner: false

nav:
  - Home: index.md
  - Getting Started:
    - Motivation: getting-started/motivation.md
    - Installation: getting-started/installation.md
    - 5-Min Quick Start: getting-started/quickstart.md
    - Tutorial: getting-started/tutorial.md
    - Key Concepts: getting-started/concepts.md
    - Preprocessing: getting-started/preprocessing.md
    - Understanding Output: getting-started/understanding-output.md
  - User Guides:
    - 🧬 Bioinformatics Workflows:
      - Create a Database: guides/create-database.md
      - Manifest Format: guides/manifest-format.md
      - Update a Database: guides/update-database.md
      - Query Allele Frequencies: guides/query.md
      - Annotate a VCF: guides/annotate-vcf.md
      - Bulk Export: guides/dump-export.md
      - Variant Info: guides/variant-info.md
      - Sample Filtering: guides/sample-filtering.md
    - 🏥 Clinical Workflows:
      - ACMG Criteria (BA1/PM2/PS4): use-cases/acmg-use-cases.md
      - Clinical Prioritization: use-cases/clinical-prioritization.md
      - Pseudo-controls: use-cases/pseudo-controls.md
      - Population-Specific AF: use-cases/population-specific-af.md
      - Sex-Specific AF: use-cases/sex-specific-af.md
      - Cohort Stratification: use-cases/cohort-stratification.md
      - Technology Integration: use-cases/technology-integration.md
  - Reference:
    - CLI Reference: reference/cli.md
    - Python API: reference/python-api.md
    - Data Model: reference/data-model.md
    - Glossary: reference/glossary.md
  - Advanced:
    - Performance Tuning: advanced/performance.md
    - Benchmarking: advanced/benchmarking.md
    - Ploidy & Special Chromosomes: advanced/ploidy-and-sex-chroms.md
    - FILTER=PASS Tracking: advanced/filter-pass-tracking.md
    - Coverage Evidence: advanced/coverage-evidence.md
    - Pipeline Integration: advanced/pipeline-integration.md
    - Multi-cohort Strategies: advanced/multi-cohort-strategies.md
    - Debugging Results: advanced/debugging-results.md
  - FAQ & Troubleshooting:
    - FAQ: faq.md
    - Troubleshooting: troubleshooting.md