Add mzIdentML 1.3 export module
- Dominant language
- Nextflow
- Stars
- 0
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
## Summary
Add MZIDENTML_EXPORT module that converts FDR-filtered results to mzIdentML 1.3. xiSEARCH path uses xi-mzidentml-converter. Scout path uses native mzIdentML export or custom converter. Required for PRIDE deposition.
## Tasks
- [ ] Create MZIDENTML_EXPORT module (modules/local/mzidentml_export/)
- [ ] Add xi-mzidentml-converter to container
- [ ] Create bin/scout_to_mzidentml.py (placeholder or Scout native)
- [ ] Publish both CSV and mzIdentML outputs
Contributor guide
Research direction
Start by examining the existing xiSEARCH and Scout workflow paths, the modules/local/mzidentml_export/ location, and the container configuration. Check how FDR-filtered results and CSV outputs are currently published, then define completion as both xiSEARCH and Scout producing mzIdentML 1.3 alongside CSV output, with the converter available in the container.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, xml
- Domain
- bioinformatics, data-engineering
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100