Update set annotations usage

[anngvu]

Close #199 and adds vignette. Let's merge this first, and then #186 will rebase to take advantage of it. This makes the necessary changes in:

• R/annotation_qc.R
• R/annotations.R
• R/calculate_related_studies.R
• R/register_study.R

While #186 makes changes in:

• R/basic_utils.R
• R/datasets.R
• R/find.R
• R/nextflow_annotation_utils.R
• R/provenance.R

[aditya-nath-sage]

Happy to test it

[aditya-nath-sage]

here is the manifest generated: https://docs.google.com/spreadsheets/d/1P4AyJyzafDRCq3sUclUdKt83mTAJIvzZPNvLKswGqU8/edit?gid=0#gid=0

Seems like most fields are still missing?

[anngvu]

@aditya-nath-sage Use the other id: syn53975003

[anngvu]

@aditya-nath-sage Reminder to 1) run through vignettes/annotate-data-intro.Rmd and 2) test annotate_with_manifest(manifest) as part of the Jira ticket NFINT-950

[aditya-nath-sage]

manifest_generate test with syn53975003 :https://docs.google.com/spreadsheets/d/1A17I4pJ9zmwf-0t1zDjVu_Ns9x20GS7ZoPL-R0EIjhk/edit?gid=0#gid=0

Seems to populate well!

[aditya-nath-sage]

Set annotations for dev project (syn26462036) and then created manifest:
Looks to have added annotations to a row!
https://docs.google.com/spreadsheets/d/1OrWpemuxs0unu2OOd23kbN5tEZyvxTXt3m1lv_8RlU8/edit?gid=0#gid=0

[anngvu]

@aditya-nath-sage Great! Thanks, this seems good enough validation that R and these package functions are clear and can be applied by you for test scenarios as well as real scenarios.

Let me know if you have any questions on "how do I use this?" or "this seems to not be working for me", otherwise you can submit review approval.