feat: expose Biosaur2 as alternative feature seeding algorithm for LFQ

[ypriverol]

Summary

Add lfq_seeding_algorithm parameter to select the feature detection seeding algorithm in ProteomicsLFQ:

• multiplex (default) — FeatureFinderMultiplex, current behavior
• biosaur2 — Biosaur2 algorithm, recently added to OpenMS (#8385)

What is Biosaur2?

A C++ reimplementation of the Biosaur2 feature detection algorithm (Abdrakhimov et al., RCMS 2022). It detects peptide features by building RT traces ("hills"), splitting at valleys, and assembling isotopic patterns with cosine scoring.

ProteomicsLFQ already tunes the Biosaur2 defaults internally (mini=500, minlh=3), so no additional parameters need to be exposed.

Changes

File	Change
modules/local/openms/proteomicslfq/main.nf	Pass -Seeding:algorithm ${params.lfq_seeding_algorithm}
nextflow.config	Add lfq_seeding_algorithm = 'multiplex'
nextflow_schema.json	Document the parameter

Test plan

• Default (multiplex) produces identical results to current version
• lfq_seeding_algorithm = 'biosaur2' runs successfully on a standard LFQ dataset

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[qodo-code-review]

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Review Summary by Qodo

Expose Biosaur2 as alternative LFQ seeding algorithm

✨ Enhancement

Walkthroughs

Description

• Add lfq_seeding_algorithm parameter to ProteomicsLFQ
• Support Biosaur2 as alternative feature detection algorithm
• Default to 'multiplex' for backward compatibility
• Document parameter in schema with enum validation

Diagram

flowchart LR
  A["lfq_seeding_algorithm parameter"] --> B["nextflow.config"]
  A --> C["nextflow_schema.json"]
  A --> D["PROTEOMICSLFQ process"]
  B --> E["Default: multiplex"]
  C --> F["Enum: multiplex, biosaur2"]
  D --> G["-Seeding:algorithm flag"]

Loading

File Changes

1. modules/local/openms/proteomicslfq/main.nf ✨ Enhancement +1/-0

Pass seeding algorithm parameter to ProteomicsLFQ

• Add -Seeding:algorithm ${params.lfq_seeding_algorithm} flag to ProteomicsLFQ command
• Positioned before -Seeding:intThreshold parameter
• Enables runtime selection of feature detection algorithm

modules/local/openms/proteomicslfq/main.nf

---

2. nextflow.config ⚙️ Configuration changes +1/-0

Add seeding algorithm configuration parameter

• Add lfq_seeding_algorithm = 'multiplex' parameter with default value
• Include inline comment explaining algorithm options
• Positioned in ProteomicsLFQ flags section

nextflow.config

---

3. nextflow_schema.json 📝 Documentation +7/-0

Document seeding algorithm parameter in schema

• Add lfq_seeding_algorithm schema definition to protein_quantification_lfq section
• Define as string type with enum constraint ['multiplex', 'biosaur2']
• Set default to 'multiplex' with descriptive help text
• Assign seedling icon for UI representation

nextflow_schema.json

---

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (0) 📎 Requirement gaps (0) 🎨 UX Issues (0)

1. Missing seeding algorithm validation 🐞 Bug ☼ Reliability

Description

PROTEOMICSLFQ injects params.lfq_seeding_algorithm directly into the ProteomicsLFQ CLI without
runtime validation (or quoting), so an invalid/empty value provided via CLI/custom config can cause
the process to fail at runtime. The enum in nextflow_schema.json and the default in
nextflow.config do not enforce correctness during execution.

Code

modules/local/openms/proteomicslfq/main.nf[51]

+        -Seeding:algorithm ${params.lfq_seeding_algorithm} \\

Evidence

The module passes the parameter straight into the shell command (`-Seeding:algorithm
${params.lfq_seeding_algorithm}`), while the schema enum is only documentation/UI and the only
runtime safeguard is a default value in nextflow.config. The repo already uses explicit
error(...) checks for invalid params elsewhere, indicating a pattern you can reuse to fail fast
with a clear message.

modules/local/openms/proteomicslfq/main.nf[38-55]
nextflow_schema.json[1054-1073]
nextflow.config[184-191]
workflows/quantms.nf[111-117]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
`params.lfq_seeding_algorithm` is passed directly to the `ProteomicsLFQ` command line. Because Nextflow schema enums are not enforced at runtime, users can still override this parameter to unsupported/empty values, leading to runtime failures with unclear tool errors.

## Issue Context
- A default is set in `nextflow.config`, but CLI overrides and custom configs can still set invalid values.
- Add a fail-fast validation (using the existing project pattern of `error(...)`) before any LFQ execution.
- Optionally quote the CLI value in the module to avoid accidental splitting if whitespace ever appears.

## Fix Focus Areas
- modules/local/openms/proteomicslfq/main.nf[38-55]
- workflows/quantms.nf[111-117]
- workflows/lfq.nf[1-120] (or wherever LFQ params are best validated)

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[jpfeuffer]

This could use some help_text on what the differences are.

[jpfeuffer]

Maybe with reference to the paper or openms tool documentation.