galaxyproject / galaxyproject/brc-analytics

FR: add option to fetch GTF from UCSC for custom workflow stepper

Open
#1,282 3 comments 0 reactions 0 assignees View on GitHub
Dominant language
TypeScript
Stars
7
Forks
11
Avg merge
2d 12h
Merged PRs (30d)
16

Description

Currently, when you use the custom workflow stepper, the second step allows picking UCSC browser tracks to include in the package, which is nice. What is less nice is that when I select the VEuPathDB gene track, I get the bigbed file imported which isn't helpful when I need GTF (well, yes, I could convert it, but since the GTF is *right there*, it would be nice if I could just select fetching it).

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by locating the custom workflow stepper and its second step, then trace how UCSC browser tracks are selected and imported. The change is complete when the VEuPathDB gene track can offer its GTF for fetching, rather than only importing the bigBed file, with the existing custom workflow behavior preserved.

Written by the indexing model from the issue text.

Assessment

Tech stack
typescript
Domain
frontend, web-dev
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
58/100

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