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Bug #17846

closed

[tutorial] inconsistencies/roadbumps

Added by Ward Vandewege almost 3 years ago. Updated 7 months ago.

Status:
Duplicate
Priority:
Normal
Assigned To:
Category:
-
Story points:
-
Release relationship:
Auto

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 1 (0 open1 closed)

Task #17875: ReviewClosedBrett Smith09/13/2023Actions

Related issues

Related to Arvados - Bug #17845: [tutorial] reuse is not workingResolvedAlex ColemanActions
Related to Arvados Epics - Idea #17001: Arvados uses WB2 by defaultResolvedActions
Related to Arvados - Support #20497: Update WGS tutorial to use Workbench 2ResolvedAlex Coleman08/16/2023Actions
Actions #1

Updated by Ward Vandewege almost 3 years ago

  • Description updated (diff)
Actions #2

Updated by Ward Vandewege almost 3 years ago

  • Related to Bug #17845: [tutorial] reuse is not working added
Actions #3

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from To Be Groomed to 2021-07-21 sprint
Actions #4

Updated by Peter Amstutz almost 3 years ago

  • Assigned To set to Ward Vandewege
Actions #5

Updated by Ward Vandewege almost 3 years 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.
Actions #6

Updated by Ward Vandewege almost 3 years ago

The plan is to

  • then point them at the output collection for the complete run (10 genomes all chromosomes)
Actions #7

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2021-07-21 sprint to 2021-08-04 sprint
Actions #8

Updated by Peter Amstutz almost 3 years ago

  • Assigned To changed from Ward Vandewege to Peter Amstutz
Actions #9

Updated by Peter Amstutz almost 3 years ago

  • Target version changed from 2021-08-04 sprint to 2021-08-18 sprint
Actions #10

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-08-18 sprint to 2021-09-01 sprint
Actions #11

Updated by Peter Amstutz over 2 years ago

  • Description updated (diff)
Actions #12

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-09-01 sprint to 2021-09-15 sprint
Actions #13

Updated by Peter Amstutz over 2 years ago

  • Assigned To deleted (Peter Amstutz)
Actions #14

Updated by Peter Amstutz over 2 years ago

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

Updated by Peter Amstutz over 2 years ago

  • Assigned To set to Peter Amstutz
Actions #16

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-09-29 sprint to 2021-10-13 sprint
  • Assigned To deleted (Peter Amstutz)
Actions #17

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-10-13 sprint to 2021-10-27 sprint
Actions #18

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-10-27 sprint to 2021-11-10 sprint
Actions #19

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-11-10 sprint to 2021-11-24 sprint
Actions #20

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-11-24 sprint to 2021-12-08 sprint
Actions #21

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2021-12-08 sprint to 2022-01-05 sprint
Actions #22

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2022-01-05 sprint to 2022-01-19 sprint
Actions #23

Updated by Peter Amstutz over 2 years ago

  • Assigned To set to Ward Vandewege
Actions #24

Updated by Peter Amstutz over 2 years ago

  • Target version changed from 2022-01-19 sprint to 2022-02-02 sprint
Actions #25

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-02-02 sprint to 2022-02-16 sprint
Actions #26

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-02-16 sprint to 2022-03-02 sprint
Actions #27

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-03-02 sprint to 2022-03-16 sprint
Actions #28

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-03-16 sprint to 2022-03-30 Sprint
Actions #29

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-03-30 Sprint to 2022-04-13 Sprint
Actions #30

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-04-13 Sprint to 2022-04-27 Sprint
Actions #31

Updated by Peter Amstutz about 2 years ago

  • Target version changed from 2022-04-27 Sprint to 2022-05-11 sprint
Actions #32

Updated by Peter Amstutz almost 2 years ago

  • Target version changed from 2022-05-11 sprint to 2022-05-25 sprint
Actions #33

Updated by Peter Amstutz almost 2 years ago

  • Target version changed from 2022-05-25 sprint to 2022-06-08 sprint
Actions #34

Updated by Peter Amstutz almost 2 years ago

  • Target version changed from 2022-06-08 sprint to 2022-07-06
Actions #35

Updated by Peter Amstutz almost 2 years ago

  • Target version changed from 2022-07-06 to 2022-07-20
Actions #36

Updated by Peter Amstutz almost 2 years ago

  • Target version changed from 2022-07-20 to 2022-08-03 Sprint
Actions #37

Updated by Peter Amstutz almost 2 years ago

  • Target version changed from 2022-08-03 Sprint to 2022-08-17 sprint
Actions #38

Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2022-08-17 sprint to 2022-08-31 sprint
Actions #39

Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2022-08-31 sprint to 2022-09-14 sprint
Actions #40

Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2022-09-14 sprint to 2022-09-28 sprint
Actions #41

Updated by Peter Amstutz over 1 year ago

  • Target version deleted (2022-09-28 sprint)
Actions #42

Updated by Peter Amstutz over 1 year ago

  • Related to Idea #17001: Arvados uses WB2 by default added
Actions #43

Updated by Peter Amstutz about 1 year ago

  • Release set to 60
Actions #44

Updated by Peter Amstutz 10 months ago

  • Assigned To deleted (Ward Vandewege)
Actions #45

Updated by Peter Amstutz 10 months ago

  • Target version set to Development 2023-07-05 sprint
  • Assigned To set to Alex Coleman
Actions #46

Updated by Peter Amstutz 10 months ago

  • Target version changed from Development 2023-07-05 sprint to Development 2023-07-19 sprint
Actions #47

Updated by Peter Amstutz 9 months ago

  • Status changed from New to In Progress
Actions #48

Updated by Peter Amstutz 9 months ago

  • Target version changed from Development 2023-07-19 sprint to Development 2023-08-02 sprint
Actions #49

Updated by Peter Amstutz 9 months ago

  • Target version changed from Development 2023-08-02 sprint to Development 2023-08-16
Actions #50

Updated by Peter Amstutz 8 months ago

  • Target version changed from Development 2023-08-16 to Development 2023-08-30
Actions #51

Updated by Peter Amstutz 8 months ago

  • Release changed from 60 to 66
Actions #52

Updated by Peter Amstutz 8 months ago

  • Target version changed from Development 2023-08-30 to Development 2023-09-13 sprint
Actions #53

Updated by Peter Amstutz 7 months ago

  • Target version changed from Development 2023-09-13 sprint to Development 2023-09-27 sprint
Actions #54

Updated by Brett Smith 7 months ago

  • Status changed from In Progress to Duplicate

Most of these have been addressed over time in other tickets. The rest are being handled in #20497. I'm closing this as basically dup.

Actions #55

Updated by Brett Smith 7 months ago

  • Related to Support #20497: Update WGS tutorial to use Workbench 2 added
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