Comprehensive documentation update for enhanced pipeline features

[edmundmiller]

Summary

Update pipeline documentation to reflect new QC metrics, analysis capabilities, and configuration options.

Tasks

• Update README with new features
• Create QC metrics interpretation guide
• Document new configuration parameters
• Add usage examples for advanced features
• Update pipeline flowchart

Dependencies

Depends on completion of feature implementation issues.

Acceptance criteria

• Complete documentation coverage
• User-friendly feature descriptions
• Configuration examples provided
• Updated pipeline diagrams