Merge pull request #5 from common-workflow-lab/jekyll-tabs-fix

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

diff --git a/_episodes/03-running.md b/_episodes/03-running.md
index 3dc317641a22b104dfa15ed98ef2c8a0560d0193..e9f740a1f2cf6a688148581bf37e64d94b8c32d0 100644 (file)
--- a/_episodes/03-running.md
+++ b/_episodes/03-running.md
@@ -31,10 +31,8 @@ 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 %}
+{% assign tabs = "generic, arvados" | split: ", " %}
+{% capture generic_tab_content %}
 main-input.yaml
 ```
 fq:
@@ -63,10 +61,9 @@ 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_tab_content %}
 main-input.yaml
 ```
 fq:
@@ -78,7 +75,7 @@ genome:
   location: keep:02a12ce9e2707610991bd29d38796b57+2912
 gtf:
   class: File
-  location: 9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
+  location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
 ```
 {: .language-yaml }
 
@@ -88,8 +85,17 @@ gtf:
 > then use the `Run CWL Workflow on Arvados` task.
 >
 {: .challenge }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+<div class="tabbed">
+  <ul class="tab">
+    {% for tab in tabs %}
+      <li><a href="#section-{{ tab }}">{{ tab }}</a></li>
+    {% endfor %}
+  </ul>
+
+  <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
+  <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
 </div>
 
 # Debugging the workflow
@@ -158,7 +164,7 @@ 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
@@ -228,3 +234,4 @@ The CWL runner will print a results JSON object to standard output.  It will loo
 This has a similar structure as `main-input.yaml`.  The each output
 parameter is listed, with the `location` field of each `File` object
 indicating where the output file can be found.
+