Let’s find the registered WGS Processing Workflow and run it interactively in our newly created project.
-# To find the registered workflow, you can search for by searching for the project "WGS Processing Tutorial", owned by "Tutorial projects", in the search box located at the top of the page. From there, select the workflow "WGS processing workflow scattered over samples".
+# To find the registered workflow, in the left-hand navigation bar, select "Public Favorites". That listing will include the "WGS Processing Workflow" project. Open that project, and it will include the workflow "WGS processing workflow scattered over samples". Open that workflow.
# Once you have found the registered workflow, you can run it your project by using the "Run Workflow" button and selecting your project ("WGS Processing Tutorial") that you set up in Section 3a, under *Project where the workflow will run*.
<figure> !{width: 100%}{{ site.baseurl }}/images/wgs-tutorial/image8.png!
<figcaption> _*Figure 7*: This is the page that pops up when you hit "Run Workflow", the input that needs selected is highlighted in yellow._ </figcaption> </figure>
h2. 5. Checking the State Of a Submitted Workflow
-Once you have submitted your workflow, you can examine its state interactively using the Arvados Workbench. If you aren’t already viewing your workflow process on the workbench, there are several ways to get to your submitted workflow. Here is the simplest way:
-
-* Via Your Project: You will want to go back to your new project, using the projects pulldown menu (the list of projects on the left) or searching for the project name. Note: You can mark a project as a favorite (if/when you have multiple projects) to make it easier to find on the pulldown menu by right-clicking on the project name on the project pulldown menu and selecting "Add to favorites".
+Once you have submitted your workflow, you can examine its state interactively using the Arvados Workbench. If you aren’t already viewing your workflow process on the workbench, you can navigate there via your project. You will want to go back to your new project, using the projects pulldown menu (the list of projects on the left) or searching for the project name. Note: You can mark a project as a favorite (if/when you have multiple projects) to make it easier to find on the pulldown menu by right-clicking on the project name on the project pulldown menu and selecting "Add to favorites".
The process you will be looking for will be titled “WGS processing workflow scattered over samples” (if you submitted via the command line/Workbench).
<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.
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
projects / arvados.git / blobdiff