Bug #17846
closed
[tutorial] inconsistencies/roadbumps
Added by Ward Vandewege over 3 years ago.
Updated over 1 year ago.
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."
- Description updated (diff)
- Related to Bug #17845: [tutorial] reuse is not working added
- Target version changed from To Be Groomed to 2021-07-21 sprint
- Assigned To set to Ward Vandewege
- 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.
The plan is to
- then point them at the output collection for the complete run (10 genomes all chromosomes)
- Target version changed from 2021-07-21 sprint to 2021-08-04 sprint
- Assigned To changed from Ward Vandewege to Peter Amstutz
- Target version changed from 2021-08-04 sprint to 2021-08-18 sprint
- Target version changed from 2021-08-18 sprint to 2021-09-01 sprint
- Description updated (diff)
- Target version changed from 2021-09-01 sprint to 2021-09-15 sprint
- Assigned To deleted (
Peter Amstutz)
- Target version changed from 2021-09-15 sprint to 2021-09-29 sprint
- Assigned To set to Peter Amstutz
- Target version changed from 2021-09-29 sprint to 2021-10-13 sprint
- Assigned To deleted (
Peter Amstutz)
- Target version changed from 2021-10-13 sprint to 2021-10-27 sprint
- Target version changed from 2021-10-27 sprint to 2021-11-10 sprint
- Target version changed from 2021-11-10 sprint to 2021-11-24 sprint
- Target version changed from 2021-11-24 sprint to 2021-12-08 sprint
- Target version changed from 2021-12-08 sprint to 2022-01-05 sprint
- Target version changed from 2022-01-05 sprint to 2022-01-19 sprint
- Assigned To set to Ward Vandewege
- Target version changed from 2022-01-19 sprint to 2022-02-02 sprint
- Target version changed from 2022-02-02 sprint to 2022-02-16 sprint
- Target version changed from 2022-02-16 sprint to 2022-03-02 sprint
- Target version changed from 2022-03-02 sprint to 2022-03-16 sprint
- Target version changed from 2022-03-16 sprint to 2022-03-30 Sprint
- Target version changed from 2022-03-30 Sprint to 2022-04-13 Sprint
- Target version changed from 2022-04-13 Sprint to 2022-04-27 Sprint
- Target version changed from 2022-04-27 Sprint to 2022-05-11 sprint
- Target version changed from 2022-05-11 sprint to 2022-05-25 sprint
- Target version changed from 2022-05-25 sprint to 2022-06-08 sprint
- Target version changed from 2022-06-08 sprint to 2022-07-06
- Target version changed from 2022-07-06 to 2022-07-20
- Target version changed from 2022-07-20 to 2022-08-03 Sprint
- Target version changed from 2022-08-03 Sprint to 2022-08-17 sprint
- Target version changed from 2022-08-17 sprint to 2022-08-31 sprint
- Target version changed from 2022-08-31 sprint to 2022-09-14 sprint
- Target version changed from 2022-09-14 sprint to 2022-09-28 sprint
- Target version deleted (
2022-09-28 sprint)
- Related to Idea #17001: Arvados uses WB2 by default added
- Assigned To deleted (
Ward Vandewege)
- Target version set to Development 2023-07-05 sprint
- Assigned To set to Alex Coleman
- Target version changed from Development 2023-07-05 sprint to Development 2023-07-19 sprint
- Status changed from New to In Progress
- Target version changed from Development 2023-07-19 sprint to Development 2023-08-02 sprint
- Target version changed from Development 2023-08-02 sprint to Development 2023-08-16
- Target version changed from Development 2023-08-16 to Development 2023-08-30
- Release changed from 60 to 66
- Target version changed from Development 2023-08-30 to Development 2023-09-13 sprint
- Target version changed from Development 2023-09-13 sprint to Development 2023-09-27 sprint
- 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.
- Related to Support #20497: Update WGS tutorial to use Workbench 2 added
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