add external link to config

revert external nav in config yml

add link to main menu

add link to page submenu

indicate external link

add id to main nav

mkdocs.yml

@@ -84,6 +84,9 @@ pages:
   - 'Bioinformatics Pipeline: Copy Number Variation Analysis': Data/Bioinformatics_Pipelines/CNV_Pipeline.md
   - 'Bioinformatics Pipeline: Methylation Liftover Pipeline': Data/Bioinformatics_Pipelines/Methylation_LO_Pipeline.md
   - Aligned Reads Summary Metrics: Data/Bioinformatics_Pipelines/Aligned_reads_summary_metrics.md
+  - GDC Reference Files: /
+  # GDC Reference Files link is replaced in nav.html
+  # with an external link
   - Release Notes: Data/Release_Notes/Data_Release_Notes.md
   - fa-file-text Download PDF /Data/PDF/Data_UG.pdf: Data/PDF/index.md
 - Encyclopedia: Encyclopedia/index.md

theme/js/gdc-common.js

@@ -504,7 +504,7 @@ $(function() {
     function _initLinks(confineToContainerID) {
       // Ensure all anchor links which appear to be external have the appropriate target and
       // icon.
-      $(confineToContainerID + ' a[href^="http"]').each(function() {
+      $(confineToContainerID + ' a[href^="http"], #main-nav a[href^="http"]').each(function() {
         var anchor = $(this);
 
         anchor.attr('target', '_blank');

theme/nav-section-map.html

@@ -7,7 +7,7 @@
 
           {% for sub_nav_item in nav_item.children %}
             <li class="{% if sub_nav_item.active %} main active{% endif %}">
-              <a href="{{ sub_nav_item.url }}">
+              <a href="{{ "https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files" if sub_nav_item.title == "GDC Reference Files" else sub_nav_item.url }}">
                 {{ sub_nav_item.title }}
               </a>
                 {% if toc and ((toc | first) is defined) and sub_nav_item.active %}

theme/nav-sub.html

@@ -1,6 +1,9 @@
 {% if not nav_item.children %}
 <li {% if nav_item.active %}class="active"{% endif %}>
-    {% if disableRootNavPrefixing %}
+    {% if nav_item.title == "GDC Reference Files" %}
+    <a
+    href="https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files">{{ nav_item.title }}</a>
+    {% elif disableRootNavPrefixing %}
     <a href="{{ nav_item.url }}">{{ nav_item.title }}</a>
     {% else %}
     <a href="{{ config.extra.project_root_dir }}{{ nav_item.url }}">{{ nav_item.title }}</a>

theme/nav.html

@@ -80,7 +80,7 @@
         <!-- Expanded navigation -->
         <div class="navbar-collapse collapse">
             <!-- Main navigation -->
-            <ul class="nav navbar-nav nav-full">
+            <ul class="nav navbar-nav nav-full" id="main-nav">
             {% for nav_item in nav %}
             {% if nav_item.title in config.extra.nav_exclude %}
             {% elif nav_item.children %}