Tags

v1.4.0

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

v1.3.1

Release v1.3.1: Complete Documentation & Interface Overhaul

✨ Major Features:
- Comprehensive CLI parameter documentation with all v1.3.1 features
- Complete elimination of documentation redundancies
- Streamlined mkdocs navigation structure
- Professional documentation standards implementation

🔧 Technical Improvements:
- Full version synchronization across all pipeline components
- Enhanced CITATION.cff with current metadata
- Cleaned repository structure with orphaned file removal
- Updated validation scripts and manifest documentation

📚 Documentation Enhancements:
- Complete parameter reference including --invert_individual, --invert_means, --prepare_jbrowse_batch
- Unified getting-started experience
- Professional changelog and version tracking
- Comprehensive usage documentation

This release focuses on documentation quality and user experience improvements
while maintaining full backward compatibility with existing workflows.

v1.3.0

v1.2.0

Release v1.2.0: BigWig Comparison Feature

Major feature release with BigWig statistical comparison capabilities:

Features:
- Statistical comparison between groups of BigWig files using deeptools bigwigCompare
- Support for log2ratio, subtract, and ratio comparison methods
- Treatment vs control comparisons via samplesheet design
- Comprehensive test suite and documentation
- Input validation utilities with improved robustness
- Enhanced pipeline architecture with modular design

Local Development Support:
- local.config for easy local testing and development
- Override HPC settings for local execution
- Windows-compatible file operations
- Reduced resource requirements for development

Documentation Updates:
- Complete user guides and API documentation
- Fixed CI/CD build errors and tool references
- Updated workflow diagrams and descriptions
- Local development setup guide

Technical Improvements:
- Modular COMPARE_BIGWIG module with clean separation
- Robust input validation and error reporting
- Organized testing framework with Python pytest integration
- Updated from wiggletools to deeptools throughout

v1.1.2

Release v1.1.2: Critical hotfix for HPC execution

Critical fixes:
- Resolved MEAN_BIGWIG input channel mismatch preventing pipeline execution
- Fixed ScriptRuntimeException on Genotoul SLURM cluster environments
- Restored missing conda environment directive in MEAN_BIGWIG module
- Ensured proper parameter passing for bin_size in mean calculation process

This hotfix is essential for pipeline execution on HPC systems.

v1.1.1

Release v1.1.1: MEAN_BIGWIG performance improvements

Key improvements:
- Replaced wiggletools with deeptools bigwigAverage for better performance
- Added configurable bin_size parameter to MEAN_BIGWIG process
- Enhanced memory efficiency and processing speed
- Updated conda environment and documentation
- Created comprehensive release notes in documentation

v1.1.0

Release v1.1.0: Enhanced documentation with interactive project info widget

Features:
- INRAE-style project information widget with toggle functionality
- Responsive design with mobile-friendly layout
- Enhanced MkDocs configuration with project metadata
- Professional pipeline overview positioning
- Custom HTML templates with CSS/JavaScript functionality
- Comprehensive project information display
- Updated documentation structure and navigation

This release provides a professional documentation experience
matching INRAE standards with interactive project information widgets.

v1.0.0

v1.0.0: Publication-ready release

🎉 First stable release with comprehensive improvements:

- Changed license to CC BY-SA 4.0 International
- Proper authorship attribution (Joseph Tran & Clara Morel)
- Enhanced CI/CD pipeline with testing and documentation
- Professional documentation with Material theme
- Academic citation support (CITATION.cff)
- Updated URLs for future INRAE repository structure

This version is ready for publication and academic use.

v0.1.0-preliminary

Preliminary working version - tested on Genotoul cluster

This version includes:
- Functional BAM to BigWig conversion pipeline
- Reorganized project structure with proper directory organization
- Working SBATCH scripts for Genotoul cluster
- Environment configurations (deeptools, conda)
- Sample sheet organization for different data sources
- Tested and validated on Genotoul infrastructure

Status: Production-ready for Genotoul cluster usage