Hackathon 2025

[SusiJo]

As part of the hackathon 2025 we can start working on these issues. Feel free to add more tasks 🚀

Documentation

• [ ] pipeline usage enhancements, i.e contrasts
• [ ] simplification and renaming of parameters (i.e. transcript length)
• [ ] update metro map

Report

• [ ] prettify report layout
• [ ] add functional plots
• [ ] add gene labels
• [ ] add visualizations (i.e. boxplots of requested gene)
• [ ] discuss splitting quarto report

Refactoring

• [ ] paramsheet vs profile
• [ ] resuming behavior
• [ ] show all params from different paramsheets
• [ ] leaderboard
• [ ] samplesheet x toolsheet = paramsheet?

Plugins

• [ ] nf-co2plugin
• [ ] nfschema
• [ ] nf-hub

Modules

• [ ] fix modules upstream and update in pipeline to remove errors, i.e. param study_name
• [ ] add propr
• [ ] preranked GSEA

[grst]

Note that we have already implemented some of the topics from "Report" in https://github.com/nf-core/differentialabundance/pull/545 (currently a bunch of merge conflicts, will update shortly).

For splitting the report, see https://github.com/nf-core/differentialabundance/pull/535