Update dev branch

[ypriverol]

User description

Pull Request

Description

Brief description of the changes made in this PR.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Performance improvement
• Code refactoring
• Test addition/update
• Updates to the dependencies has been done.

---

PR Type

Documentation

---

Description

• Auto-update MultiQC report HTML files with new timestamps

• Update compressed plot data in multiple report documents

• Regenerate report UUIDs for tracking purposes

• Refresh configuration creation dates across reports

---

Diagram Walkthrough

flowchart LR
  A["MultiQC Reports"] -- "Update timestamps" --> B["Report HTML Files"]
  A -- "Regenerate UUIDs" --> B
  A -- "Refresh plot data" --> B
  B -- "Updated configs" --> C["Documentation"]

Loading

File Walkthrough

	Relevant files
Documentation	4 files multiqc_report.html Update report UUID and timestamps                                                +4/-4      multiqc_report.html Update report UUID and timestamps                                                +4/-4      multiqc_report.html Update report UUID and timestamps                                                +4/-4      multiqc_report.html Update report UUID and timestamps                                                +4/-4
Additional files	16 files multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +6/-6      multiqc_report.html +6/-6      multiqc_report.html +4/-4      multiqc_report.html +5/-5      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +4/-4      multiqc_report.html +5/-5      multiqc_report.html +4/-4

---

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[qodo-code-review]

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
⚪	Embedded data exposure Description: The updated mqc_compressed_plotdata blob is an opaque embedded dataset that could unintentionally contain sensitive identifiers (e.g., sample names, file paths, run metadata) and should be verified as safe for publication before merging. multiqc_report.html [26-26] Referred Code <script type="text/plain" id="mqc_compressed_plotdata">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</script>
Ticket Compliance
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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: 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: 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

Compliance status legend

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

[qodo-code-review]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
High-level	Avoid committing auto-generated report files The suggestion advises against committing auto-generated report files to the repository. Instead, it recommends generating them in a CI/CD pipeline and publishing them as artifacts to avoid repository bloat and improve reviewability. Examples: docs/PXD066146/multiqc_report.html [1-1219] docs/PXD054720/multiqc_report.html [1-1219] Solution Walkthrough: Before: # Repository Structure /docs /PXD066146 - multiqc_report.html # Large, generated report file /PXD054720 - multiqc_report.html # Another large, generated report file ... # PR action: # Manually re-generate reports and commit the changes. # The PR diff contains massive changes to these HTML files. After: # Repository Structure (after applying suggestion) /docs /PXD066146 # multiqc_report.html is removed from git /PXD054720 # multiqc_report.html is removed from git ... /.github/workflows/generate_reports.yml # New CI/CD pipeline # on: push # jobs: # build_docs: # - run: generate_multiqc_reports.sh # - uses: actions/upload-artifact # with: # name: multiqc-reports # path: docs/ Suggestion importance[1-10]: 9 __ Why: This is a critical suggestion addressing a fundamental repository management anti-pattern, as committing large, auto-generated files makes the repository bloated and PRs unreviewable.	High
General	Use correct JSON script type Change the script type from text/plain to application/json to correctly identify the embedded JSON data. docs/PXD066146/multiqc_report.html [26] -<script type="text/plain" id="mqc_compressed_plotdata">H4sIAEx0W2kA/... +<script type="application/json" id="mqc_compressed_plotdata">H4sIAEx0W2kA/... ...</script> [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies that type="text/plain" is not ideal for JSON data and proposes type="application/json", which is a best practice for semantic correctness and parser compatibility.	Medium
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