galaxyproject / galaxyproject/brc-analytics
ENA picker refinements
- Dominant language
- TypeScript
- Stars
- 7
- Forks
- 11
- Avg merge
- 2d 12h
- Merged PRs (30d)
- 16
Description
# Case 1: Finding SRA data for a particular organism
In this scenario a user selects an organism and proceeds to configure Galaxy inputs clicking "Browse all 466 Sequences"
> [!CAUTION]
> "Browse all 466 Sequences" should **really** say "Browse all 466 Sequences for this organism"
This given this table:
One of the first things one needs here is to figure out what BioProjects are available
Here are important things to make it very useful:
- Naturally this list needs to be sorted by size in the descending order
- Project IDs should be clickable and these links should go to something like this https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1174053, which will open in a new Tab of the browser. This will allow quickly decide whether this is relevant or not
- Can columns of the Run viewer be sortable? (even better: can some summary stats [max,min] be shown there?)
- It should be possible to download the table as a tsv,csv
- We need to add additional validation for paired-end data: In some cases the datasets sas it is paired but it actually not:
Here ERR2352345 is paired but SRR175719 is not. We see that by the number of entries in "Fastq FTP" field. In other words, when we select "Paired" in the filter we need to make sure that "Library Layout" == "Paired" and len("Fastq FTP".split(',')) > 1. Otherwise we get this:
Contributor guide
No contributing guide indexed for this repository
Assessment
This issue has not been assessed yet.