This project aims to address open issues and improve the nf-core/hic pipeline for Hi-C data analysis. We will address the milestones for the release of pipeline version 2.2.0.
The nf-core/hic pipeline processes Hi-C data to analyze chromatin 3D organization. With 42+ open issues covering bugs, enhancements, and feature requests, this hackathon project provides opportunities to contribute at all levels.
We welcome contributors of all experience levels!
Goals
Bug fixes
- Fix parameter type errors (#229:
--res_zoomifytype validation) - Resolve MultiQC reporting issues (#221: not all samples reported)
- Fix compressed genome file handling (#215: GET_RESTRICTION_FRAGMENTS)
- Address bowtie2 version compatibility (#208)
- Resolve COOLER_MAKEBINS process errors (#218)
- Fix FastQ splitting errors (#198)
- And more…
Enhancements
- Improve Arima Hi-C protocol support (#225)
- Add loop calling tools (#189)
- Improve MultiQC report (#190)
- Compress output files (.allValidPairs, .txt) (#220)
- Implement replicate merging functionality (#223)
- Add pairtools protocol support (#162)
Documentation and usability
- Update documentation to reflect current pipeline state
- Improve error messages
- Add examples for common use cases
Recommended preparation
To help you get the most out of this project, we suggest completing these Nextflow training modules beforehand:
Resources
location
ZS Copenhagen
category
pipelines
