20497: Give brief instructions for reviewing subprocess output

[arvados.git] / doc / user / tutorials / wgs-tutorial.html.textile.liquid

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 396f82b4685f1528ef1daf07abbfbd660082b1db..8513f0fc7b026aa0e00a707afb0ac70647858078 100644 (file)
--- a/doc/user/tutorials/wgs-tutorial.html.textile.liquid
+++ b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
@@ -220,9 +220,7 @@ Once your workflow has finished, you can see how long it took the workflow to ru
 <figure> !{width: 100%}{{ site.baseurl }}/images/wgs-tutorial/image5.png!
 <figcaption> _*Figure 8*:  A completed workflow process in Arvados as viewed via the Arvados Workbench. You can click on the outputs link (highlighted in yellow) to view the outputs. Outputs of a workflow are stored in a collection._ </figcaption> </figure>
 
-If we click on the outputs of the workflow, we will see the output collection.
-
-Contained in this collection, is the GVCF, tabix index file, and html ClinVar report for each analyzed sample (e.g. set of FASTQs).  You can directly open it in the browser by selecting the file listing. Additionally, by clicking on the download button to the right of the file, you can download it to your local machine.  You can also use the command line to download single files or whole collections to your machine. You can examine the outputs of a step similarly by using the arrow to expand the panel to see more details.
+If we click on the outputs of the workflow, we will see the output collection. It contains the GVCF, tabix index file, and HTML ClinVar report for each analyzed sample (e.g. set of FASTQs). You can open a report in the browser by selecting it from the listing. You can also download a file to your local machine by right-clicking a file and selecting "Download" from the context menu, or from the action menu available from the far right of each listing.
 
 Logs for the main process can be found back on the workflow process page. Selecting the "LOGS" button at the top navigates down to the logs. You can view the logs directly through that panel, or in the upper right-hand corner select the button with hover-over text "Go to Log collection". 
 There several logs available, so here is a basic summary of what some of the more commonly used logs contain.  Let's first define a few terms that will help us understand what the logs are tracking.
@@ -348,6 +346,8 @@ The tail end of our log should be similar to the following:
 
 This is the command we ran to invoke bwa-mem, and the scaling information for running bwa-mem multi-threaded across 16 cores (15.4x).
 
+You can also view outputs for the subprocess just like you do for the main workflow process. Back on the subprocess page for *bwamem-samtools-view_2*, the Outputs pane shows the output files of this specific subprocess. In this case, it is a single BAM file. This way, if your workflow succeeds but produces a surprising result, you can download and review the intermediate outputs to investigate further.
+
 We hope that now that you have a bit more familiarity with the logs you can continue to use them to debug and optimize your own workflows as you move forward with using Arvados if your own work in the future.
 
 h2. 7.  Conclusion