---
title: "Running and Debugging a Workflow"
-teaching: 10
+teaching: 15
exercises: 20
questions:
- "How do I provide input to run a workflow?"
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 %}
main-input.yaml
-
```
fq:
class: File
> ```
> cwl-runner main.cwl main-input.yaml
> ```
+> {: .language-bash }
>
> This may take a few minutes to run, and will print some amount of
> logging. The logging you see, how access other logs, and how to
> track workflow progress will depend on your CWL runner platform.
+{: .challenge }
+{% endcapture %}
+
+{% capture arvados_tab_content %}
+main-input.yaml
+```
+fq:
+ class: File
+ location: keep:9178fe1b80a08a422dbe02adfd439764+925/raw_fastq/Mov10_oe_1.subset.fq
+ format: http://edamontology.org/format_1930
+genome:
+ class: Directory
+ location: keep:02a12ce9e2707610991bd29d38796b57+2912
+gtf:
+ class: File
+ location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
+```
+{: .language-yaml }
+
+> ## Running the workflow
+>
+> If you are using VSCode with Arvados tasks, select `main.cwl` and
+> then use the `Run CWL Workflow on Arvados` task.
>
-> {: .language-bash }
{: .challenge }
+{% 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
* tmpdirMin: temporary directory available space
* outdirMin: output directory available space
-After setting the RAM requirements, re-run the workflow.
+> ## Running the workflow
+>
+> Now that you've fixed the workflow, run it again.
+>
+{: .challenge }
+
+> ## Episode solution
+> * <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 %}
+
+{% tab output generic %}
```
{
"bam_sorted_indexed": {
}
```
{: .language-yaml }
+{% endtab %}
+
+{% tab output arvados %}
+```
+{
+ "bam_sorted_indexed": {
+ "basename": "Aligned.sortedByCoord.out.bam",
+ "class": "File",
+ "location": "keep:2dbaaef5aefd558e37f14280e47091a9+327/Aligned.sortedByCoord.out.bam",
+ "secondaryFiles": [
+ {
+ "basename": "Aligned.sortedByCoord.out.bam.bai",
+ "class": "File",
+ "location": "keep:2dbaaef5aefd558e37f14280e47091a9+327/Aligned.sortedByCoord.out.bam.bai"
+ }
+ ],
+ "size": 25370695
+ },
+ "qc_html": {
+ "basename": "Mov10_oe_1.subset_fastqc.html",
+ "class": "File",
+ "location": "keep:2dbaaef5aefd558e37f14280e47091a9+327/Mov10_oe_1.subset_fastqc.html",
+ "size": 383589
+ }
+}
+```
+{: .language-yaml }
+{% endtab %}
+{% endtabs %}
+</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.
+
+<script>
+ (function() {
+ // Get relevant elements and collections
+ const tabbed = document.querySelector('.tabbed');
+ const tablist = tabbed.querySelector('ul');
+ const tabs = tablist.querySelectorAll('a');
+ const panels = tabbed.querySelectorAll('[id^="section"]');
+
+ // The tab switching function
+ const switchTab = (oldTab, newTab) => {
+ newTab.focus();
+ // Make the active tab focusable by the user (Tab key)
+ newTab.removeAttribute('tabindex');
+ // Set the selected state
+ newTab.setAttribute('aria-selected', 'true');
+ newTab.classList.add('active');
+ oldTab.removeAttribute('aria-selected');
+ oldTab.setAttribute('tabindex', '-1');
+ oldTab.classList.remove('active');
+ // Get the indices of the new and old tabs to find the correct
+ // tab panels to show and hide
+ let index = Array.prototype.indexOf.call(tabs, newTab);
+ let oldIndex = Array.prototype.indexOf.call(tabs, oldTab);
+ panels[oldIndex].hidden = true;
+ panels[index].hidden = false;
+ }
+
+ // Add the tablist role to the first <ul> in the .tabbed container
+ tablist.setAttribute('role', 'tablist');
+
+ // Add semantics are remove user focusability for each tab
+ Array.prototype.forEach.call(tabs, (tab, i) => {
+ tab.setAttribute('role', 'tab');
+ tab.setAttribute('id', 'tab' + (i + 1));
+ tab.setAttribute('tabindex', '-1');
+ // tab.setAttribute('class', 'active');
+ tab.parentNode.setAttribute('role', 'presentation');
+
+ // Handle clicking of tabs for mouse users
+ tab.addEventListener('click', e => {
+ e.preventDefault();
+ let currentTab = tablist.querySelector('[aria-selected]');
+ if (e.currentTarget !== currentTab) {
+ switchTab(currentTab, e.currentTarget);
+ }
+ });
+
+ // Handle keydown events for keyboard users
+ tab.addEventListener('keydown', e => {
+ // Get the index of the current tab in the tabs node list
+ let index = Array.prototype.indexOf.call(tabs, e.currentTarget);
+ // Work out which key the user is pressing and
+ // Calculate the new tab's index where appropriate
+ let dir = e.which === 37 ? index - 1 : e.which === 39 ? index + 1 : e.which === 40 ? 'down' : null;
+ if (dir !== null) {
+ e.preventDefault();
+ // If the down key is pressed, move focus to the open panel,
+ // otherwise switch to the adjacent tab
+ dir === 'down' ? panels[i].focus() : tabs[dir] ? switchTab(e.currentTarget, tabs[dir]) : void 0;
+ }
+ });
+ });
+
+ // Add tab panel semantics and hide them all
+ Array.prototype.forEach.call(panels, (panel, i) => {
+ panel.setAttribute('role', 'tabpanel');
+ panel.setAttribute('tabindex', '-1');
+ let id = panel.getAttribute('id');
+ panel.setAttribute('aria-labelledby', tabs[i].id);
+ panel.hidden = true;
+ });
+
+ // Initially activate the first tab and reveal the first tab panel
+ tabs[0].removeAttribute('tabindex');
+ tabs[0].setAttribute('aria-selected', 'true');
+ tabs[0].setAttribute('class', 'active');
+ panels[0].hidden = false;
+ })();
+</script>
projects / rnaseq-cwl-training.git / blobdiff