Comprehensive documentation update for enhanced pipeline features

## 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