mkdocs.yml

site_name: Viralgenie
repo_name: Joon-Klaps/viralgenie
repo_url: https://github.com/Joon-Klaps/viralgenie
site_url: https://joon-klaps.github.io/viralgenie/latest/

nav:
  - Home:
      - "Introduction": README.md
      - "Installation": installation.md
      - "Usage": usage.md
      - "Output": output.md
      - "Citations": CITATIONS.md
  - Quick Start: quickstart.md
  - Workflow:
      - "Pipeline overview": workflow/overview.md
      - "Preprocessing": workflow/preprocessing.md
      - "Metagenomic diversity": workflow/metagenomic_diversity.md
      - "Assembly & Polishing": workflow/assembly_polishing.md
      - "Variant analysis & Iterative refinement": workflow/variant_and_refinement.md
      - "Consensus evaluation": workflow/consensus_qc.md
  - Parameters: "parameters.md"
  - Customisation:
      - "Databases": customisation/databases.md
      - "Configuration": customisation/configuration.md
  - Contributing: "CONTRIBUTING.md"

theme:
  name: material
  favicon: images/ViralGenie-nf-core-theme.png
  logo: images/ViralGenie-nf-core-theme.png
  palette:
    - media: "(prefers-color-scheme)"
      primary: custom
      accent: custom
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      # scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: material/weather-sunny
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: material/weather-night
        name: Switch to system preference
  font:
    text: "Ubuntu"
    code: "Ubuntu Mono"
  features:
    - announce.dismiss
    - content.action.edit
    - content.code.annotate
    - content.code.copy
    - header.autohide
    - navigation.footer
    - navigation.instant
    - navigation.sections
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.share
    - search.suggest
    - toc.follow
extra_css:
  - stylesheets/extra.css
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css

extra_javascript:
  - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
  - javascripts/tablesort.js
  - javascripts/katex.js
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js

markdown_extensions:
  - admonition
  - attr_list
  - def_list
  - tables
  - md_in_html
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.critic
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.details
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.arithmatex:
      generic: true
# plugins:
#   - search
#   - social:
#       cards: !ENV [CARDS, true]

extra:
  version:
    provider: mike
  analytics:
    provider: google
    property: G-DJ9PDTBEEC
    feedback:
      title: Was this page helpful?
      ratings:
        - icon: material/heart
          name: This page was helpful
          data: 1
          note: >-
            Thanks for your feedback, I like you too!
        - icon: material/heart-broken
          name: This page could be improved
          data: 0
          note: >-
            Thanks for your feedback! Help us improve this page by
            submitting an <a href="https://github.com/Joon-Klaps/viralgenie/issues/new/?labels=website%2Cdocumentation&template=website_feedback.yml&title=[Website feedback]+{title}" target="_blank" rel="noopener">issue</a>.
  consent:
    title: Cookie Consent
    description: >-
      We use cookies to recognize your repeated visits and preferences, as well
      as to measure the effectiveness of our documentation and whether users
      find what they're searching for. With your consent, you're helping us to
      make our documentation better.
  social:
    - icon: fontawesome/brands/x-twitter
      link: https://twitter.com/LemeyLab
    - icon: fontawesome/brands/github
      link: https://github.com/Joon-Klaps