Fix contaminant_affix help text to match default value

[Copilot]

• Understand the issue: The contaminant_affix option has default value CONT but help text says CONT_
• Fix help text to match the actual default value of CONT
• Verify the fix
• Run code review and security checks (no issues found)
• Verify CONT default works across all plugins (MaxQuant, DIA-NN, quantms, mzidentml)

Original prompt

On cli.py:41-41, Looks like the default value for contaminant affix is CONT, but in the help it says CONT_. Can you change it to CONT as default if that is the case.

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PR Type

Bug fix

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Description

• Fixed help text for --contaminant_affix option

• Corrected default value documentation from CONT_ to CONT

• Aligns help text with actual default parameter value

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Diagram Walkthrough

flowchart LR
  A["Help text<br/>default: CONT_"] -- "correction" --> B["Help text<br/>default: CONT"]
  C["Actual default<br/>CONT"] -- "now matches" --> B

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File Walkthrough

	Relevant files
Bug fix	cli.py Correct contaminant_affix help text default value                pmultiqc/cli.py Updated contaminant_affix option help text Changed default value documentation from CONT_ to CONT Ensures help text matches the actual default parameter value +1/-1

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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
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Custom Compliance
🟢	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: 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: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
⚪	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: No logging change: The new code only updates CLI help text and does not impact or add any audit logging for critical actions, which may be acceptable given the scope but cannot be verified from this diff alone. Referred Code default="CONT", help="The contaminant prefix or suffix used or to be used (default: CONT)", ) 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: No error paths: The change only updates help text for a CLI option and adds no error handling, which is likely out of scope but cannot confirm robustness from this diff alone. Referred Code default="CONT", help="The contaminant prefix or suffix used or to be used (default: CONT)", ) 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: Input validation scope: The modification only adjusts CLI help text and does not add or alter input validation; adequacy of validation for the option cannot be determined from this diff. Referred Code default="CONT", help="The contaminant prefix or suffix used or to be used (default: CONT)", ) 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
General	Automatically show default value in help Use the show_default=True parameter in the click.option to automatically display the default value and remove the hardcoded default from the help string. pmultiqc/cli.py [39-40] default="CONT", -help="The contaminant prefix or suffix used or to be used (default: CONT)", +show_default=True, +help="The contaminant prefix or suffix used or to be used.", Apply / Chat Suggestion importance[1-10]: 7 __ Why: The suggestion correctly proposes using show_default=True to prevent the kind of inconsistency between the default value and the help text that this PR is fixing, thus improving maintainability.	Medium
More

[ypriverol]

@copilot can you make sure that in fact for all the plugins the default value CONT works?

[Copilot]

@copilot can you make sure that in fact for all the plugins the default value CONT works?

I verified that the default value CONT works across all plugins:

• MaxQuant plugin: Uses "potential contaminant" column with "+" values from the MaxQuant file format - doesn't use contaminant_affix parameter.
• DIA-NN plugin: Basic contaminant handling via a different mechanism.
• quantms plugin: Uses contaminant_affix with str.contains() for filtering protein accessions containing the affix.
• mzidentml plugin: Similar approach to quantms.

The CONT default works correctly because:

1. It matches accessions like CONT_P12345
2. It also matches CONTAMINANT_* accessions (since they contain CONT)

All 15 existing tests pass. The CLI help now correctly shows (default: CONT) (commit 71f4530).