[arvados] updated: 2.6.0-280-g1c0fefc8ec

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Summary of changes:
 doc/user/tutorials/wgs-tutorial.html.textile.liquid | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

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       via  ef2d81c44fd0df585d89265859e36e23e1bc567b (commit)
       via  249df8a49b8a6f0e52a10515d787ee19f7ff6c14 (commit)
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commit 1c0fefc8ec275b53d4adef0546e2c3b8847d8b93
Author: Brett Smith <brett.smith at curii.com>
Date:   Mon Sep 18 10:35:42 2023 -0400

    20497: Give brief instructions for reviewing subprocess output
    
    This was previously discussed in the same paragraph as the main workflow
    download collection. Moving it here means we don't jump back and forth
    as much between the main workflow process and a subprocess.
    
    Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 1eb3de84b5..8513f0fc7b 100644
--- a/doc/user/tutorials/wgs-tutorial.html.textile.liquid
+++ b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
@@ -346,6 +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

commit 9bc1495877f624d3d0787384f7cbddc6aedd8bab
Author: Brett Smith <brett.smith at curii.com>
Date:   Mon Sep 18 09:37:52 2023 -0400

    20497: Clarify collection view/download
    
    Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 396f82b468..1eb3de84b5 100644
--- 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.

commit 09489ada444106d040898c9e013a3cdb00328432
Author: Brett Smith <brett.smith at curii.com>
Date:   Mon Sep 18 09:34:55 2023 -0400

    20497: Clean up section 5 opening paragraph
    
    There used to be multiple navigation options listed here. Now that
    there's only one, the introduction needs to be updated to match.
    
    Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 017f170be6..396f82b468 100644
--- a/doc/user/tutorials/wgs-tutorial.html.textile.liquid
+++ b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
@@ -196,9 +196,7 @@ Now, you are ready to check the state of your submitted workflow.
 
 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).
 

commit 89573e33f317da0633acce7b4160435e20318ca7
Author: Brett Smith <brett.smith at curii.com>
Date:   Mon Sep 18 09:31:14 2023 -0400

    20497: Direct the reader to the tutorial project via Public Favorites
    
    Unfortunately searching for the project raises a couple of issues:
    
    * The search results return two copies of the project, one from pirca
      and one from jutro. If the reader picks the jutro one, they'll be
      prompted to log in again, losing their progress and kicking them off the
      happy path.
    
    * The search results also return the finished demo workflow process we
      publish for people, "(start here) Example WGS processing workflow". This
      is attractive to people because it says "(start here)", has a bright
      green "Completed" badge next to it, and the difference between a process
      and a project may not be clear to people who are just getting started
      with Arvados.
    
    Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 19c8f6ad83..017f170be6 100644
--- a/doc/user/tutorials/wgs-tutorial.html.textile.liquid
+++ b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
@@ -114,7 +114,7 @@ We have already previously registered the WGS workflow and set default input val
 
 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>

commit ef2d81c44fd0df585d89265859e36e23e1bc567b
Author: Brett Smith <brett.smith at curii.com>
Date:   Mon Sep 18 09:29:24 2023 -0400

    20497: Add missing paragraph break
    
    Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 1dd70d0e4d..19c8f6ad83 100644
--- a/doc/user/tutorials/wgs-tutorial.html.textile.liquid
+++ b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
@@ -230,6 +230,7 @@ Logs for the main process can be found back on the workflow process page. Select
 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.
 
 As you may recall, Arvados Crunch manages the running of workflows. A _container request_ is an order sent to Arvados Crunch to perform some computational work. Crunch fulfils a request by either choosing a worker node to execute a container, or finding an identical/equivalent container that has already run. You can use _container request_ or _container_ to distinguish between a work order that is submitted to be run and a work order that is actually running or has been run. So our container request in this case is just the submitted workflow we sent to the Arvados cluster.
+
 A _node_ is a compute resource where Arvardos can schedule work.  In our case since the Arvados Playground is running on a cloud, our nodes are virtual machines.  @arvados-cwl-runner@ (acr) executes CWL workflows by submitting the individual parts to Arvados as containers and crunch-run is an internal component that runs on nodes and executes containers.
 
 * @stderr.txt@

commit 249df8a49b8a6f0e52a10515d787ee19f7ff6c14
Author: Brett Smith <brett.smith at curii.com>
Date:   Mon Sep 18 09:28:20 2023 -0400

    20497: Make button text consistent with Workbench 2 UI
    
    Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>

diff --git a/doc/user/tutorials/wgs-tutorial.html.textile.liquid b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
index 983f522f15..1dd70d0e4d 100644
--- a/doc/user/tutorials/wgs-tutorial.html.textile.liquid
+++ b/doc/user/tutorials/wgs-tutorial.html.textile.liquid
@@ -67,7 +67,7 @@ Projects in Arvados help you organize and track your work - and can contain data
 To create a new project, go to the Projects dropdown menu and select the "+NEW" button, then select “New project”.
 
 <figure> !{width: 100%}{{ site.baseurl }}/images/wgs-tutorial/image4.png!
-<figcaption> _*Figure 3*:  Adding a new project using Arvados Workbench, select the "+NEW" button in the upper left-hand corner and click "New Project"._ </figcaption> </figure>
+<figcaption> _*Figure 3*:  Adding a new project using Arvados Workbench, select the "+NEW" button in the upper left-hand corner and click "New project"._ </figcaption> </figure>
 
 Let’s name your project “WGS Processing Tutorial”. You can also add a description of your project by typing in the **Description - optional** field. The universally unique identifier (UUID) of the project can be found in the URL, or by clicking the info button on the upper right-hand corner.
 
@@ -108,7 +108,7 @@ In this section, we will be discussing three ways to run the tutorial workflow u
 
 h3. 4a. Interactively Running a Workflow Using Workbench
 
-Workflows can be registered in Arvados. Registration allows you to share a workflow with other Arvados users, and let’s them run the workflow by clicking the  "+ New" button and selecting "Run a workflow" on the Workbench Dashboard or on the command line by specifying the workflow UUID.  Default values can be specified for workflow inputs.
+Workflows can be registered in Arvados. Registration allows you to share a workflow with other Arvados users, and let’s them run the workflow by clicking the  "+NEW" button and selecting "Run a workflow" on the Workbench Dashboard or on the command line by specifying the workflow UUID.  Default values can be specified for workflow inputs.
 
 We have already previously registered the WGS workflow and set default input values for this set of the walkthrough.
 

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