_quarto.yml

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

website:
  title: "Single cell transcriptomics"
  favicon: assets/SIB_logo.svg
  search: true
  page-navigation: true
  # google-analytics: G-1H5B39PY7V
  # cookie-consent: true
  navbar:
    background: "#003eaa"
    left:
      - href: index.qmd
        text: Home
      - href: precourse_preparations.qmd
      - href: course_schedule.qmd
      - text: "day 1"
        menu:
          - href: "day1/day1-1_setup.qmd"
          - href: "day1/day1-1a_cellranger.qmd"
          - href: "day1/day1-2_analysis_tools_qc.qmd"
          - href: "day1/day1-3_normalization_scaling.qmd"
      - text: "day 2"
        menu: 
          - href: "day2/day2-1_dimensionality_reduction.qmd"
          - href: "day2/day2-2_integration.qmd"
          - href: "day2/day2-3_clustering.qmd"
          - href: "day2/day2-4_cell_annotation.qmd"
      - text: "day 3"
        menu:
          - href: "day3/day3-1_differential_gene_expression.qmd"
          - href: "day3/day3-2_enrichment_analysis.qmd"
          - href: "day3/day3-3_trajectory_analysis.qmd"
          - href: "day3/day3-4_advanced_analyses.qmd"
          
    right:
      - icon: github
        href: https://github.com/sib-swiss/single-cell-training/
        aria-label: GitHub
  sidebar:
    logo: assets/SIB_LogoQ_GBv.svg

format:
  html:
    code-link: true
    theme: 
      - default
      - custom.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