update quantms-rescoring and support AalphaPeptDeep model

[daichengxin]

User description

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• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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PR Type

Enhancement

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Description

• Update quantms-rescoring container to version 0.0.11

• Rename ms2pip parameters to generic ms2 model parameters

• Support AlphaPeptDeep model integration

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Diagram Walkthrough

flowchart LR
  A["Container Update"] --> B["Parameter Rename"]
  B --> C["AlphaPeptDeep Support"]
  C --> D["Enhanced MS2 Rescoring"]

Loading

File Walkthrough

	Relevant files
Configuration changes	modules.config Rename ms2pip parameter to generic ms2 model                          conf/modules/modules.config Update parameter name from --ms2pip_model to --ms2_model +1/-1      nextflow.config Update parameter names for generic model support                  nextflow.config Rename ms2pip_model_dir to ms2_model_dir Rename ms2pip_model to ms2_model +2/-2      nextflow_schema.json Update schema for renamed parameters                                          nextflow_schema.json Update schema to reflect parameter name changes Change description to generic ms2 prediction model +3/-3
Enhancement	main.nf Update container version and parameter names                          modules/local/utils/msrescore_features/main.nf Update container to quantms-rescoring:0.0.11 Change parameter from ms2pip_model_dir to ms2_model_dir +3/-3

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[qodo-code-review]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Parameter Consistency The parameter name change from ms2pip_model to ms2_model should be verified to ensure all references are updated consistently across the codebase and that the underlying tool supports this parameter name. "--ms2_model ${params.ms2_model}", "--calibration_set_size ${params.calibration_set_size}", Container Update The container version update from 0.0.10 to 0.0.11 should be validated to ensure compatibility with the parameter changes and that the new version supports AlphaPeptDeep model integration as mentioned in the PR description. 'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.11' : 'ghcr.io/bigbio/quantms-rescoring:0.0.11' }"

[qodo-code-review]

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[Copilot]

Pull Request Overview

Updates the quantms-rescoring container to version 0.0.11 and renames MS2PiP-specific parameters to generic MS2 model parameters to support AlphaPeptDeep model integration.

• Update quantms-rescoring container from 0.0.10 to 0.0.11
• Rename ms2pip parameters to generic ms2 model parameters for broader model support
• Add new mask_modloss parameter for controlling modloss ion masking in MS2 prediction models

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
modules/local/utils/msrescore_features/main.nf	Updates container version and implements ms2_model_dir parameter change with new mask_modloss functionality
nextflow.config	Renames ms2pip parameters to generic ms2 model parameters and adds mask_modloss configuration
nextflow_schema.json	Updates parameter schema definitions to reflect the renamed parameters and adds mask_modloss schema
conf/modules/modules.config	Updates module configuration to use the new ms2_model parameter name