galaxyproject / galaxyproject/brc-analytics

ENA picker refinements

Open
#723 3 comments 0 reactions 3 assignees Claimed by @MillenniumFalconMechanic View on GitHub
roadmap item
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"

Image

This given this table:

Image

One of the first things one needs here is to figure out what BioProjects are available

Image

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:

Image

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:

Image

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.