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- 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.
- Confusingly for the user, there is also that visible run https://workbench.pirca.arvadosapi.com/container_requests/pirca-xvhdp-0ipx8626jkb7qob#Status which is called "(start here) Example WGS processing workflow" and shows up in the same search query. Should we rename the latter to something less confusing if we do not actually want people to start there? As far as I can tell that visible run is (only?) intended to make reuse work (but, see #17845).
- 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."
#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
- have people run 5 genome chromosome 19 (with reuse enabled, so that we can show scatter). Jiayong has a collection. Here's the yml: https://github.com/arvados/arvados-tutorial/blob/main/WGS-processing/yml/wgs-processing-wf-chr19.yml
- then point them at the output collection for the complete run (10 genomes all chromosomes)