Phase 2: Add QuantUMS, timsTOF, and phosphoproteomics parameters

[ypriverol]

Description of feature

Add DIA-NN parameter wiring to existing modules (no workflow structure changes). These are low-risk additions that users can immediately test.

Tasks

2a. QuantUMS Quantification (v1.9+)

ML-optimized quantification. Applied in FINAL_QUANTIFICATION only.

New params:

Parameter	Type	Default	Description
quantums	boolean	false	Enable QuantUMS mode
quantums_train_runs	string	null	Run range for training (e.g., "0:5")
quantums_sel_runs	integer	null	Auto-select N runs for training
quantums_params	string	null	Pre-calculated QuantUMS parameters

Files: modules/local/diann/final_quantification/main.nf, nextflow.config, nextflow_schema.json

2b. Synchro-PASEF / timsTOF Flags (v1.9+)

Addresses #440.

New params:

Parameter	Type	Default	DIA-NN Flag
diann_tims_sum	boolean	false	--quant-tims-sum
diann_im_window	number	null	--im-window

Pass to PRELIMINARY_ANALYSIS, ASSEMBLE_EMPIRICAL_LIBRARY, INDIVIDUAL_ANALYSIS (all steps reading raw data). Not FINAL_QUANTIFICATION (uses --use-quant).

2c. Phospho: --monitor-mod Auto-detection (v1.9.2+)

Addresses #510, #334.

When variable modifications include phosphorylation (UniMod:21), auto-append --monitor-mod UniMod:21 to diann_config.cfg.

New params: diann_monitor_mod (string, default: null) — explicit override

Files: quantmsutils/diann/dianncfg.py, modules/local/diann/final_quantification/main.nf

2d. Phospho: Peptidoform Scoring Control (v1.9.2+)

Addresses #640 (user asked about --no-peptidoforms).

New params: diann_no_peptidoforms (boolean, default: false)
Pass to PRELIMINARY_ANALYSIS and INDIVIDUAL_ANALYSIS.

2e. Phospho: Site-Level Quantification (v2.0+)

New params: diann_site_ms1_quant (boolean, default: false) → --site-ms1-quant
Capture .site_report.parquet as optional output from FINAL_QUANTIFICATION.

Test Plan

• Run PXD026600 with --quantums true and DIA-NN >= 2.1.0 — verify QuantUMS activates
• Run PXD037766 (Synchro-PASEF, timsTOF Pro 2) with --diann_tims_sum true
• Run PXD070420 (phospho DIA by Vadim Demichev) — verify --monitor-mod UniMod:21 auto-detected
• Run PXD026600 with --diann_no_peptidoforms true — verify flag passed correctly

Test Datasets:

Dataset	Feature	Instrument
PXD026600	QuantUMS	Orbitrap (existing CI/CD)
PXD037766	Synchro-PASEF	timsTOF Pro 2
PXD061613	diaPASEF/Synchro	timsTOF HT
PXD070420	Phospho DIA	ZenoTOF 7600 + timsTOF Ultra
PXD067491	Phospho 4D-DIA	Orbitrap Fusion