2024-12-06

CLIMB-COVID · Dec 6, 2024 · dd6988e · dd6988e
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diff --git a/CNAME b/CNAME
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+status.covid19.climb.ac.uk
diff --git a/_config.yml b/_config.yml
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+title: CLIMB-COVID Status
+theme: jekyll-theme-minimal
+logo: assets/climb-covid-patch.png
+logo_alt: CLIMB-COVID Mission Patch
diff --git a/_includes/summary.html b/_includes/summary.html
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+<h2>Summary</h2>
+
+<span style="font-size: 2em">69</span>
+<h3>Genomes today</h3>
+
+<span style="font-size: 2em">3505355</span>
+<h3>Genomes total</h3>
+
+<hr>
+
+<h2>Figures</h2>
+
+<a href="#service-status">Service status by date</a></br>
+<a href="#daily-genomes">Genomes by published date</a></br>
+<a href="#collection-genomes">Genomes by collection date</a></br>
+<a href="#total-genomes">Cumulative processed genomes</a></br>
diff --git a/_layouts/default.html b/_layouts/default.html
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+<!DOCTYPE html>
+<html lang="{{ site.lang | default: "en-US" }}">
+  <head>
+    <meta charset="UTF-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+
+{% seo %}
+    <link rel="stylesheet" href="{{ "/assets/css/style.css?v=" | append: site.github.build_revision | relative_url }}">
+    <!--[if lt IE 9]>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
+    <div class="wrapper">
+      <header>
+        {% if site.logo %}
+          <img src="{{site.logo | relative_url}}" alt="{{site.logo_alt}}" width="200px" style="margin: 0 0 20px 0" />
+        {% endif %}
+
+        {% include summary.html %}
+        <hr>
+
+        {% if site.github.is_project_page %}
+        <p class="view"><a href="{{ site.github.repository_url }}">View the Project on GitHub <small>{{ site.github.repository_nwo }}</small></a></p>
+        {% endif %}
+
+        {% if site.github.is_user_page %}
+        <p class="view"><a href="{{ site.github.owner_url }}">View My GitHub Profile</a></p>
+        {% endif %}
+
+      </header>
+      <section>
+
+      {{ content }}
+
+      </section>
+      <footer>
+        {% if site.github.is_project_page %}
+        <p>This project is maintained by <a href="{{ site.github.owner_url }}">{{ site.github.owner_name }}</a></p>
+        {% endif %}
+        <p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
+      </footer>
+    </div>
+    <script src="{{ "/assets/js/scale.fix.js" | relative_url }}"></script>
+    {% if site.google_analytics %}
+    <script>
+      (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+      (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+      m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+      })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
+      ga('create', '{{ site.google_analytics }}', 'auto');
+      ga('send', 'pageview');
+    </script>
+    {% endif %}
+  </body>
+</html>
diff --git a/assets/climb-covid-patch.png b/assets/climb-covid-patch.png
diff --git a/assets/cog-uk.png b/assets/cog-uk.png
diff --git a/assets/css/style.scss b/assets/css/style.scss
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+---
+---
+
+$header-bg-color: #8B7968;
+$section-headings-color: #8B7968;
+
+@import 'jekyll-theme-minimal';
+
+.wrapper {
+    width: 1200px;
+    margin: 0 auto;
+}
+
+header {
+    width: 20%;
+    float: left;
+    position: inherit;
+    -webkit-font-smoothing: subpixel-antialiased;
+}
+
+section {
+    width: 75%;
+    float: right;
+    padding-bottom: 50px;
+}
+
+footer {
+    float: left;
+}
+
+@media print, screen and (max-width: 480px) {
+    header {
+        width: auto;
+    }
+}
+@media print, screen and (max-width: 720px) {
+    header {
+        width: auto;
+    }
+}
+@media print, screen and (max-width: 960px) {
+    header {
+        width: auto;
+    }
+}
diff --git a/assets/touch b/assets/touch
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+
diff --git a/graphs/fig1.assembled.png b/graphs/fig1.assembled.png
diff --git a/graphs/fig1b.png b/graphs/fig1b.png
diff --git a/graphs/fig1c.png b/graphs/fig1c.png
diff --git a/graphs/fig2.png b/graphs/fig2.png
diff --git a/graphs/s1.png b/graphs/s1.png
diff --git a/index.md b/index.md
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+<div align="center">
+    <h2 align="center">CLIMB-COVID Status Report</h2>
+    <h1 align="center">2024-12-06</h1>
+</div>
+
+***
+
+## <a name="service-status"></a>[Service status by date](#service-status)
+
+<img src="graphs/fig2.png" width="100%">
+
+## <a name="daily-genomes"></a>[Processed genomes by published date](#daily-genomes)
+
+<img src="graphs/fig1b.png" width="100%">
+
+
+## <a name="collection-genomes"></a>[Processed genomes by sample collection date](#collection-genomes)
+
+<img src="graphs/fig1c.png" width="100%">
+
+
+## <a name="total-genomes"></a>[Cumulative processed genomes](#total-genomes)
+
+<img src="graphs/fig1.assembled.png" width="100%">
diff --git a/report_date b/report_date
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+2024-12-06