Show arvados sections by default, instead of generic ones.

[rnaseq-cwl-training.git] / _episodes / 03-running.md

diff --git a/_episodes/03-running.md b/_episodes/03-running.md
index 0cf63605d3c3d2d7927918b6855d5446fe45ebd6..9c627149e201d1b8a64aa73ddc439f38a5bc8791 100644 (file)
--- a/_episodes/03-running.md
+++ b/_episodes/03-running.md
@@ -31,10 +31,7 @@ plain strings that may or may not be file paths.
 
 Note: if you don't have example sequence data or the STAR index files, see [setup](/setup.html).
 
-<div>
-{% tabs input %}
-
-{% tab input generic %}
+{% capture generic_input_tab_content %}
 main-input.yaml
 ```
 fq:
@@ -63,10 +60,9 @@ gtf:
 > logging.  The logging you see, how access other logs, and how to
 > track workflow progress will depend on your CWL runner platform.
 {: .challenge }
+{% endcapture %}
 
-{% endtab %}
-
-{% tab input arvados %}
+{% capture arvados_input_tab_content %}
 main-input.yaml
 ```
 fq:
@@ -88,8 +84,16 @@ gtf:
 > then use the `Run CWL Workflow on Arvados` task.
 >
 {: .challenge }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+<div class="tabbed">
+  <ul class="tab">
+      <li><a href="#section-arvados-input">arvados</a></li>
+      <li><a href="#section-generic-input">generic</a></li>
+  </ul>
+
+  <section id="section-arvados-input">{{ arvados_input_tab_content | markdownify}}</section>
+  <section id="section-generic-input">{{ generic_input_tab_content | markdownify}}</section>
 </div>
 
 # Debugging the workflow
@@ -158,17 +162,15 @@ Resource requirements you can set include:
 {: .challenge }
 
 > ## Episode solution
-> * <a href="{% link assets/answers/ep3/main.cwl %}">main.cwl</a>
+> * <a href="../assets/answers/ep3/main.cwl">main.cwl</a>
 {: .solution}
 
 # Workflow results
 
 The CWL runner will print a results JSON object to standard output.  It will look something like this (it may include additional fields).
 
-<div>
-{% tabs output %}
+{% capture generic_output_tab_content %}
 
-{% tab output generic %}
 ```
 {
     "bam_sorted_indexed": {
@@ -194,9 +196,9 @@ The CWL runner will print a results JSON object to standard output.  It will loo
 }
 ```
 {: .language-yaml }
-{% endtab %}
+{% endcapture %}
 
-{% tab output arvados %}
+{% capture arvados_output_tab_content %}
 ```
 {
     "bam_sorted_indexed": {
@@ -221,8 +223,16 @@ The CWL runner will print a results JSON object to standard output.  It will loo
 }
 ```
 {: .language-yaml }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+<div class="tabbed">
+  <ul class="tab">
+      <li><a href="#section-arvados-output">arvados</a></li>
+      <li><a href="#section-generic-output">generic</a></li>
+  </ul>
+
+  <section id="section-arvados-output">{{ arvados_output_tab_content | markdownify}}</section>
+  <section id="section-generic-output">{{ generic_output_tab_content | markdownify}}</section>
 </div>
 
 This has a similar structure as `main-input.yaml`.  The each output