Fix trailing whitespace and code formatting

[Copilot]

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).

Changes

Code formatting and cleanup:

• Trailing whitespace: Fixed trailing space on line 205 of workflows/quantms.nf
• Prettier validation: Verified all yml, yaml, json, and md files pass prettier formatting checks
• Syntax updates: Applied language server hint recommendations
• Channel chaining: Cleaned up file staging logic

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PR Type

Bug fix

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Description

• Remove trailing whitespace on line 205

• Clean up formatting in quantms.nf workflow file

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Diagram Walkthrough

flowchart LR
  A["quantms.nf<br/>line 205"] -- "remove trailing space" --> B["Clean formatting"]

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File Walkthrough

	Relevant files
Formatting	quantms.nf Remove trailing whitespace in workflow file                            workflows/quantms.nf Remove trailing whitespace after .collect() on line 205 Maintain consistent code formatting in multiqc_inputs channel definition +1/-1

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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: 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 audit signals: The changes only adjust formatting and do not add or affect any auditing/logging of critical actions, making compliance unverifiable from this diff alone. Referred Code // create cross product of all inputs multiqc_inputs = CREATE_INPUT_CHANNEL.out.ch_expdesign .mix(ch_pipeline_results.ifEmpty([])) .mix(ch_multiqc_files.collect()) .mix(ch_ids_pmultiqc.collect().ifEmpty([])) .mix(ch_consensus_pmultiqc.collect().ifEmpty([])) .mix(ch_msstats_in.ifEmpty([])) .collect() SUMMARY_PIPELINE( multiqc_inputs, ch_multiqc_quantms_logo, ) 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 logic: The diff only removes trailing whitespace and does not introduce or modify any error handling, so compliance cannot be assessed from the added lines. Referred Code // create cross product of all inputs multiqc_inputs = CREATE_INPUT_CHANNEL.out.ch_expdesign .mix(ch_pipeline_results.ifEmpty([])) .mix(ch_multiqc_files.collect()) .mix(ch_ids_pmultiqc.collect().ifEmpty([])) .mix(ch_consensus_pmultiqc.collect().ifEmpty([])) .mix(ch_msstats_in.ifEmpty([])) .collect() SUMMARY_PIPELINE( multiqc_inputs, ch_multiqc_quantms_logo, ) 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: No input validation: The added changes are purely formatting and do not touch input validation or data handling, so security validation compliance cannot be determined from this diff segment. Referred Code // create cross product of all inputs multiqc_inputs = CREATE_INPUT_CHANNEL.out.ch_expdesign .mix(ch_pipeline_results.ifEmpty([])) .mix(ch_multiqc_files.collect()) .mix(ch_ids_pmultiqc.collect().ifEmpty([])) .mix(ch_consensus_pmultiqc.collect().ifEmpty([])) .mix(ch_msstats_in.ifEmpty([])) .collect() SUMMARY_PIPELINE( multiqc_inputs, ch_multiqc_quantms_logo, ) Learn more about managing compliance generic rules or creating your own custom rules

Compliance status legend

🟢 - Fully Compliant
🟡 - Partial Compliant
🔴 - Not Compliant
⚪ - Requires Further Human Verification
🏷️ - Compliance label

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