Note: if you don't have example sequence data or the STAR index files, see [setup](/setup.html).
-{% assign tabs = "generic, arvados" | split: ", " %}
-{% capture generic_tab_content %}
+{% capture generic_input_tab_content %}
main-input.yaml
```
fq:
{: .challenge }
{% endcapture %}
-{% capture arvados_tab_content %}
+{% capture arvados_input_tab_content %}
main-input.yaml
```
fq:
<div class="tabbed">
<ul class="tab">
- {% for tab in tabs %}
- <li><a href="#section-{{ tab }}">{{ tab }}</a></li>
- {% endfor %}
+ <li><a href="#section-generic-input">generic</a></li>
+ <li><a href="#section-arvados-input">arvados</a></li>
</ul>
- <section id="section-generic">{{ generic_tab_content | markdownify}}</section>
- <section id="section-arvados">{{ arvados_tab_content | markdownify}}</section>
+ <section id="section-generic-input">{{ generic_input_tab_content | markdownify}}</section>
+ <section id="section-arvados-input">{{ arvados_input_tab_content | markdownify}}</section>
</div>
# Debugging the workflow
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": {
}
```
{: .language-yaml }
-{% endtab %}
+{% endcapture %}
-{% tab output arvados %}
+{% capture arvados_output_tab_content %}
```
{
"bam_sorted_indexed": {
}
```
{: .language-yaml }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+<div class="tabbed">
+ <ul class="tab">
+ <li><a href="#section-generic-output">generic</a></li>
+ <li><a href="#section-arvados-output">arvados</a></li>
+ </ul>
+
+ <section id="section-generic-output">{{ generic_output_tab_content | markdownify}}</section>
+ <section id="section-arvados-output">{{ arvados_output_tab_content | markdownify}}</section>
</div>
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.
-