Update the django app to report "raw reads" for a sequence lane.

[htsworkflow.git] / htsworkflow / frontend / templates / samples / library_detail.html

diff --git a/htsworkflow/frontend/templates/samples/library_detail.html b/htsworkflow/frontend/templates/samples/library_detail.html
index 3533477506e6420e87387d5891923129e50a0419..4c5c2b889e678a65edd3fb94eef06c0a2a6ddbab 100644 (file)
--- a/htsworkflow/frontend/templates/samples/library_detail.html
+++ b/htsworkflow/frontend/templates/samples/library_detail.html
@@ -1,7 +1,4 @@
 {% load humanize %}
-
-<hr/>
-<br/>
 <style type="text/css">
   /* <![CDATA[ */
   table, td {
@@ -26,11 +23,50 @@
   /* ]]> */
 </style>
 
+<h2>About this library</h2>
+<b>Library ID</b>: {{ lib.library_id }}<br/>
+<b>Name</b>: {{ lib.library_name }}<br/>
+<b>Species</b>: {{ lib.library_species.scientific_name }}<br/>
+<b>Affiliations</b>:
+<ul>
+  {% for individual in lib.affiliations.all %}
+    <li>{{ individual.name }} ( {{ individual.contact }} )</li>
+  {% endfor %}
+</ul>
+
+<h2>Raw Result Files</h2>
+<table>
+<thead>
+  <tr>
+    <td>Cycle</td>
+    <td>Flowcell</td>
+    <td>Lane</td>
+    <td>Summary</td>
+    <td>Eland</td>
+    <td>Bed</td>
+  </tr>
+{% for result in eland_results %}
+<tr>
+  <td>{{ result.cycle }}</td>
+  <td>{{ result.flowcell_id }}</td>
+  <td>{{ result.lane }}</td>
+  <td><a href="{{ result.summary_url }}">Summary</a></td>
+  <td><a href="{{ result.result_url }}">{{ result.result_label }}</a></td>
+  <td>
+  {% if result.bed_url %}
+    <a href="{{ result.bed_url }}">Bed</a>
+  {% endif %}
+  </td>
+</tr>
+{% endfor %}
+</table>
+
+<h2>Lane Summary Statistics</h2>
 {% block summary_stats %}
 <table>
   <thead>
     <tr>
-      <td colspan="6"></td>
+      <td colspan="7"></td>
       <td colspan="2">No Match</td>
       <td colspan="2">QC Failed</td>
       <td colspan="4">Unique</td>
@@ -42,6 +78,7 @@
     <td>Lane</td>
     <td>End</td>
     <td>Cluster / Tile</td>
+    <td>pM</td>
     <td>Raw Reads</td>
     <td>total</td>
     <td>%</td>
@@ -66,6 +103,7 @@
       <td>{{ lane.lane_id }}</td>
       <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
       <td>{{ lane.clusters.0|intcomma }}</td>
+      <td>{{ lane.successful_pm }}</td>
       <td>{{ lane.reads|intcomma }}</td>
       <td>{{ lane.no_match|intcomma }}</td>
       <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
@@ -85,15 +123,18 @@
 </table>
 <br/>
 <hr/>
+<h2>Count of multi-reads</h2>
 {% for lane in lane_summary_list %}
-<h2>
-  {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }} 
-  {% if lane.end %} end {{ lane.end }}{% endif %}
-</h2>
+  {% if lane.summarized_reads %}
+  <h3>
+    {{lane.cycle_width}} {{ lane.flowcell_id }} lane {{ lane.lane_id }} 
+    {% if lane.end %} end {{ lane.end }}{% endif %}
+  </h3>
   <ul>
     {% for name, counts in lane.summarized_reads.items %}
     <li><b>{{ name }}</b>: {{ counts|intcomma }}</li>
     {% endfor %}
   </ul>
+  {% endif %}
 {% endfor %}
 {% endblock %}