mkdocs.yml

site_name: gbcms
site_description: High-performance variant counting from BAM files
site_author: MSK-ACCESS
site_url: https://msk-access.github.io/gbcms/

repo_name: msk-access/gbcms
repo_url: https://github.com/msk-access/gbcms
edit_uri: edit/main/docs/

theme:
  name: material
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.sections
    - navigation.expand
    - navigation.top
    - navigation.indexes
    - navigation.path
    - toc.follow
    - content.code.copy
    - content.code.annotate
    - search.suggest
    - search.highlight

plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\,(?!\d)|&[lg]t;'
  - mermaid2:
      version: "11.4.0"
  - mkdocs-pdf
  - glightbox:
      touchNavigation: true
      loop: false
      effect: zoom
      zoomable: true
      draggable: true
  - git-revision-date-localized:
      enable_creation_date: true
      enable_git_follow: false
      fallback_to_build_date: true
      type: timeago
  - panzoom:
      full_screen: True
      always_show_hint: false
      key: "none"
  # print-site provides /print_page/ — all docs combined for browser-based PDF.
  # Must be last.
  - print-site:
      add_to_navigation: false
      print_page_title: "gbcms Documentation"
      add_table_of_contents: false
      enumerate_headings: false
      add_cover_page: true
      add_full_urls: false
      include_css: true

nav:
  - Home: index.md
  
  - Getting Started:
    - Choose Your Mode: getting-started/index.md
    - Installation: getting-started/installation.md
    - Quick Start: getting-started/quickstart.md
  
  - CLI Reference:
    - Overview: cli/index.md
    - DNA Command: cli/dna.md
    - RNA Command: cli/rna.md
    - Merge Command: cli/merge.md
    - Normalize Command: cli/normalize.md
  
  - Nextflow Pipeline:
    - Overview: nextflow/index.md
    - Samplesheet: nextflow/samplesheet.md
    - Parameters: nextflow/parameters.md
    - Examples: nextflow/examples.md
  
  - How It Works:
    - Architecture: reference/architecture.md
    - Input Formats: reference/input-formats.md
    - Output Formats: reference/output-formats.md
    - Variant Normalization: reference/variant-normalization.md
    - Read Filters: reference/read-filters.md
    - RNA Splice Handling: reference/rna-splice-handling.md
    - RNA Annotation: reference/rna-annotation.md
    - Allele Classification: reference/allele-classification.md
    - Counting & Metrics: reference/counting-metrics.md
    - mFSD Report: reference/mfsd-report.md
    - Complex Indels: reference/complex-indels.md
    - Glossary: reference/glossary.md
  
  - Development:
    - Developer Guide: development/developer-guide.md
    - Testing Guide: development/testing-guide.md
    - Release Guide: development/release-guide.md
    - Changelog: development/changelog.md
    - Contributing: development/contributing.md
  
  - Resources:
    - Troubleshooting: resources/troubleshooting.md
    - Citation: resources/citation.md

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:mermaid2.fence_mermaid_custom
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets:
      base_path:
        - .
        - docs
      auto_append:
        - includes/abbreviations.md
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

extra_css:
  - stylesheets/extra.css

extra:
  generator: false
  version:
    provider: mike
    default: stable
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/msk-access/gbcms

copyright: |
  Developed by <a href="https://github.com/rhshah">Ronak H Shah</a> @ 
  <a href="https://www.mskcc.org">MSKCC</a> | 
  Built with <a href="https://antigravity.google/">Antigravity</a> | 
  <a href="https://github.com/msk-access/gbcms/blob/main/LICENSE">AGPL-3.0</a>