v1.0.4-mod

🌳 Added Standalone Tree Grafting Tool

• graft_trees.py: Standalone Python script for tree grafting when the main workflow fails
  • Robust leaf-expansion grafting algorithm using Biopython
  • Detailed logging and error reporting
  • Conflict resolution for tip label collisions
  • Dry-run capability for testing
  • Memory-efficient alternative to Nextflow-based grafting

FirstRelease

# wf-assembly-snps-mod v1.0.3-mod

A enhanced version of the bacterial genome assembly SNP identification workflow with scalable and recombination-aware analysis modes.

## 🚀 New Features
- **Scalable Mode**: Analyze hundreds to thousands of genomes efficiently
- **Recombination-Aware Mode**: Enhanced phylogenetic accuracy  
- **Comprehensive Documentation**: Complete parameter reference and usage guides
- **Convenience Wrapper**: Easy-to-use script for common workflows

## 📊 Key Improvements
- Divide-and-conquer clustering for large datasets
- Optimized Gubbins integration
- Multiple compute environment profiles
- Enhanced error handling and logging

## 📖 Documentation
See the comprehensive [README.md](README.md) for detailed usage instructions and the [CHANGELOG.md](CHANGELOG.md) for complete modification details.

## 🙏 Acknowledgments
Built upon the excellent foundation of [bacterial-genomics/wf-assembly-snps](https://github.com/bacterial-genomics/wf-assembly-snps).