Bug #17846

[tutorial] inconsistencies/roadbumps

Added by Ward Vandewege 3 months ago. Updated 5 days ago.

Status:
New
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
Due date:
% Done:

0%

Estimated time:
(Total: 0.00 h)
Story points:
-

Description

This is about https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html:

  • the tutorial says to search for the “PGP UK FASTQs” collection, but that collection does not exist, there is "PGP UK FASTQs (one genome)" and "PGP UK FASTQs (ten genomes)". Which of these 2 collections should the tutorial to refer to?
  • the tutorial says to search for the "WGS Processing Workflow” registered workflow. There is a project with that name at https://workbench.pirca.arvadosapi.com/projects/pirca-j7d0g-chdv0xwrzxngtfn, which contains the workflow "WGS processing workflow scattered over samples". It would be better to point directly at that workflow from the tutorial docs (i.e. change the search term), if that is indeed the intended one. We don't explain that one needs to navigate from the project to the registered workflow in it, and in any case, that is an unnecessary step.
  • The tutorial says "The input Directory of paired FASTQ files will need to be set. " but that is not true, it defaults to "keep:a146a06222f9a66b7d141e078fc67660+376237". The registered workflow should be updated to make that input field empty.
  • Customer feedback - "Hi all - I'm going through the users guide and discovered a discrepency in steps. Specifically https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html, from step 3a setting up a new project to step 3b working with collections. There is no transition.
    EDIT: Nevermind, its there, just wasn't clear as II was reading it."

Subtasks

Task #17875: ReviewNewWard Vandewege


Related issues

Related to Arvados - Bug #17845: [tutorial] reuse is not workingNew

History

#1 Updated by Ward Vandewege 3 months ago

  • Description updated (diff)

#2 Updated by Ward Vandewege 3 months ago

  • Related to Bug #17845: [tutorial] reuse is not working added

#3 Updated by Peter Amstutz 3 months ago

  • Target version changed from To Be Groomed to 2021-07-21 sprint

#4 Updated by Peter Amstutz 2 months ago

  • Assigned To set to Ward Vandewege

#5 Updated by Ward Vandewege 2 months ago

  • there is a bugfix for the fastq quality generation (the output doesn't get saved). Fix has been pushed to the arvados-tutorial repo (blog-examples branch). Sarah to point Peter at the fix, and Peter will take care of that.
  • we should switch to just using Chrom 19. Peter will take care of that.

#6 Updated by Ward Vandewege 2 months ago

The plan is to

  • then point them at the output collection for the complete run (10 genomes all chromosomes)

#7 Updated by Peter Amstutz 2 months ago

  • Target version changed from 2021-07-21 sprint to 2021-08-04 sprint

#8 Updated by Peter Amstutz 2 months ago

  • Assigned To changed from Ward Vandewege to Peter Amstutz

#9 Updated by Peter Amstutz 2 months ago

  • Target version changed from 2021-08-04 sprint to 2021-08-18 sprint

#10 Updated by Peter Amstutz about 2 months ago

  • Target version changed from 2021-08-18 sprint to 2021-09-01 sprint

#11 Updated by Peter Amstutz about 1 month ago

  • Description updated (diff)

#12 Updated by Peter Amstutz 19 days ago

  • Target version changed from 2021-09-01 sprint to 2021-09-15 sprint

#13 Updated by Peter Amstutz 19 days ago

  • Assigned To deleted (Peter Amstutz)

#14 Updated by Peter Amstutz 19 days ago

  • Target version changed from 2021-09-15 sprint to 2021-09-29 sprint

#15 Updated by Peter Amstutz 5 days ago

  • Assigned To set to Peter Amstutz

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