X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/0cc762dafead8f398e8d0b67bd29774a8f988ae0..fe18c05b5fc565ce4a82370d1df110b62655e72f:/_episodes/03-running.md
diff --git a/_episodes/03-running.md b/_episodes/03-running.md
index 47f7aab..b7c6bb4 100644
--- 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).
-
-{% 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:
@@ -88,8 +85,17 @@ gtf:
> then use the `Run CWL Workflow on Arvados` task.
>
{: .challenge }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+
+
+ {% for tab in tabs %}
+ - {{ tab }}
+ {% endfor %}
+
+
+
{{ generic_tab_content | markdownify}}
+
{{ arvados_tab_content | markdownify}}
# Debugging the workflow
@@ -228,3 +234,83 @@ 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.
+
+