_quarto.yml

project:
  type: website
  execute-dir: project
  render:
    - "*.qmd"
    - "!CONTRIBUTIONG.md"
    - "!LICENSE.md"

website:
  title: "Cancer variant analysis"
  favicon: assets/SIB_logo.svg
  search: true
  page-navigation: true
  navbar:
    background: "#003eaa"
    left:
      - href: index.qmd
        text: Home
      - href: precourse_preparations.qmd
      - href: course_schedule.qmd
      - text: 'Course material'
        menu:
            - href: quality_control.qmd
            - href: variant_calling.qmd
            - href: variant_annotation.qmd 
          
    right:
      - icon: github
        href: https://github.com/sib-swiss/cancer-variants-training/
        aria-label: GitHub
  sidebar:
    logo: assets/SIB_LogoQ_GBv.svg

format:
  html:
    code-link: true
    theme: 
      light:
        - default
        - custom.scss
      dark: 
        - darkly
        - custom-dark.scss
    toc: true
    header-includes: |
      <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Source+Sans+Pro">
      <!-- Matomo -->
      <script>
        var _paq = window._paq = window._paq || [];
        /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
        _paq.push(['trackPageView']);
        _paq.push(['enableLinkTracking']);
        (function() {
          var u="https://matomo.sib.swiss/";
          _paq.push(['setTrackerUrl', u+'matomo.php']);
          _paq.push(['setSiteId', '220']);
          var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
          g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
        })();
      </script>
      <!-- End Matomo Code -->


execute:
  freeze: auto 
  cache: true
  tidy: true