bigbio / bigbio/relink

Add mzIdentML 1.3 export module

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Nextflow
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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

Open the contributing 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

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