X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/fe18c05b5fc565ce4a82370d1df110b62655e72f..2f8029fae95be67664dde4e8c40d7ef15fd64631:/_episodes/03-running.md
diff --git a/_episodes/03-running.md b/_episodes/03-running.md
index b7c6bb4..9c62714 100644
--- a/_episodes/03-running.md
+++ b/_episodes/03-running.md
@@ -31,8 +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).
-{% assign tabs = "generic, arvados" | split: ", " %}
-{% capture generic_tab_content %}
+{% capture generic_input_tab_content %}
main-input.yaml
```
fq:
@@ -63,7 +62,7 @@ gtf:
{: .challenge }
{% endcapture %}
-{% capture arvados_tab_content %}
+{% capture arvados_input_tab_content %}
main-input.yaml
```
fq:
@@ -89,13 +88,12 @@ gtf:
-
{{ generic_tab_content | markdownify}}
-
{{ arvados_tab_content | markdownify}}
+
+
# Debugging the workflow
@@ -171,10 +169,8 @@ Resource requirements you can set include:
The CWL runner will print a results JSON object to standard output. It will look something like this (it may include additional fields).
-
-{% tabs output %}
+{% capture generic_output_tab_content %}
-{% tab output generic %}
```
{
"bam_sorted_indexed": {
@@ -200,9 +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": {
@@ -227,90 +223,18 @@ The CWL runner will print a results JSON object to standard output. It will loo
}
```
{: .language-yaml }
-{% endtab %}
-{% endtabs %}
+{% endcapture %}
+
+
+
+
+
{{ arvados_output_tab_content | markdownify}}
+
{{ generic_output_tab_content | markdownify}}
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.
-
-