v1.4.0: Major CLI Simplification & Enhanced Reproducibility 🎯 Simplified Command-Line Interface: - Boolean flags no longer require explicit true/false values - Auto-enabled comparison analysis when comparison_design provided - Unified invert_reverse parameter replaces separate individual/means flags - JBrowse parameter consolidation to single prepare_jbrowse_batch flag 🔬 Enhanced Execution Environment Reporting: - Comprehensive software version tracking (samtools, deeptools, bedtools) - Complete environment snapshot for reproducibility - Enhanced HTML/JSON/TXT reports with execution environment details 💡 User Experience Improvements: - Intuitive CLI following standard conventions - Reduced parameter complexity and better error handling - Updated test scripts and comprehensive documentation - Complete project documentation and CLI examples updated to v1.4.0