small changes for release

[ypriverol]

User description

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the bigbio/quantms branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

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PR Type

Enhancement, Documentation

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Description

• Change logging level from info to warn for MS2pip warnings

• Update CHANGELOG with DIA pipeline mzTab default parameter change

• Document deprecation of luciphor parameters in favor of onsite

• Add entries for recent pipeline updates and improvements

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Diagram Walkthrough

flowchart LR
  A["Logging Changes"] -->|info to warn| B["MS2pip Warnings"]
  C["CHANGELOG Updates"] -->|Added| D["DIA mzTab Default"]
  C -->|Added| E["Deprecations Section"]
  E -->|luciphor params| F["onsite params"]

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File Walkthrough

	Relevant files
Enhancement	main.nf Upgrade MS2pip warnings to warn level                                        modules/local/utils/msrescore_features/main.nf Changed log.info to log.warn for MS2pip unit compatibility warnings Improves log severity classification for warning messages Two instances updated in conditional branches +2/-2
Documentation	CHANGELOG.md Document parameter changes and deprecations                            CHANGELOG.md Added entry for PR some updates related with diann, ptms and pmultiqc small issues #614 documenting DIA pipeline mzTab default parameter change Created new "Deprecations" section documenting removal of luciphor-specific parameters Documented replacement with unified onsite parameters for PTM localization Clarifies migration path for users from luciphor to onsite module +5/-0

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[qodo-code-review]

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢	No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
Ticket Compliance
⚪	🎫 No ticket provided Create ticket/issue
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
🟢	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
⚪	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Unstructured log message: The newly added log.warn messages are plain-text and may not meet the checklist requirement for structured logging (e.g., JSON), though this may be constrained by Nextflow logging conventions. Referred Code log.warn "Warning: MS2pip only supports Da unit. Using default from config!" ms2_tolerance = 0.05 } else { log.warn "Warning: MS2pip only supports Da unit. Using default from config!" } Learn more about managing compliance generic rules or creating your own custom rules
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⚪ - Requires Further Human Verification
🏷️ - Compliance label

[qodo-code-review]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	✅ Assign default value after warning Suggestion Impact: The commit updated the warning-handling branches so that after logging the warning, `ms2_tolerance` is explicitly set to the configured default (`params.ms2features_tolerance`). While it did not hardcode `0.05` as suggested, it implemented the intent of assigning a default value consistent with the warning message. code diff: + } else if (fragment_unit_lower == 'ppm' || params.ms2features_tolerance_unit == 'ppm') { log.warn "Warning: MS2pip only supports Da unit. Using default from config!" - ms2_tolerance = 0.05 + ms2_tolerance = params.ms2features_tolerance } else { - log.warn "Warning: MS2pip only supports Da unit. Using default from config!" + log.warn "Warning: MS2pip only supports Da unit. Fragment mass tolerance unit '${meta['fragmentmasstoleranceunit']}' is not supported. Using default from config! In the future, please use 'Da' or 'ppm'." + ms2_tolerance = params.ms2features_tolerance } In the else block, assign the default value 0.05 to ms2_tolerance after logging the warning to ensure the code's behavior matches the warning message. modules/local/utils/msrescore_features/main.nf [56-58] } else { log.warn "Warning: MS2pip only supports Da unit. Using default from config!" + ms2_tolerance = 0.05 } [Suggestion processed] Suggestion importance[1-10]: 9 __ Why: This suggestion correctly identifies and fixes a bug where a warning message indicates a default value is used, but the code does not actually assign it, potentially leading to incorrect calculations.	High
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