NEWS

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Capsule 0.2.0 (2025-11-11)

Major Update: Bioinformatics Focus

This release adds comprehensive support for bioinformatics and computational biology workflows, with enhancements specifically designed for NGS analysis, HPC environments, and large-scale data processing.

New Features - Critical for Bioinformatics

• External Tool Version Tracking

  • track_external_tools(): Track versions of command-line tools (samtools, STAR, BWA, etc.)
  • get_tool_versions(): Retrieve tracked tool versions
  • Automatically detects and tracks 18+ common bioinformatics tools

• Conda/Mamba Environment Support

  • track_conda_env(): Export and track conda environments
  • restore_conda_env(): Restore conda environments from YAML
  • get_conda_env_info(): Retrieve conda environment information
  • Full support for both conda and mamba

• Reference Genome Tracking

  • track_reference_genome(): Track reference genomes, annotations, and indices
  • get_reference_info(): Retrieve reference genome information
  • list_reference_sources(): Display common reference genome sources
  • Tracks FASTA files, GTF/GFF annotations, and aligner indices (STAR, BWA, etc.)

New Features - High Priority

• Large File Handling

  • Enhanced track_data() with smart checksumming for large files (>1GB)
  • xxHash64 support for 10-100x faster checksumming of BAM/FASTQ files
  • Metadata-based fingerprinting for very large files
  • Automatic algorithm selection based on file size

• System Library Detection

  • capture_system_libraries(): Detect system library versions
  • Tracks libcurl, libxml2, BLAS/LAPACK implementations
  • Essential for documenting system dependencies

• Hardware Information Capture

  • capture_hardware(): Capture CPU, RAM, and GPU specifications
  • NVIDIA GPU detection via nvidia-smi
  • Cross-platform support (Linux, macOS, Windows)
  • Essential for HPC job documentation

New Features - Containerization & HPC

• Singularity/Apptainer Support
  • generate_singularity(): Generate Singularity definition files
  • Full support for HPC environments where Docker is unavailable
  • Automatic build script generation
  • Conda environment integration

New Features - Pipeline Integration

• Workflow Manager Integration
  • export_for_nextflow(): Export data for Nextflow pipelines
  • export_for_snakemake(): Export data for Snakemake workflows
  • export_for_wdl(): Export data for WDL workflows
  • export_for_cwl(): Export data for CWL workflows
  • Seamless integration with major workflow managers

New Features - Snapshot Management

• Snapshot Comparison
  • compare_snapshots(): Compare two workflow snapshots
  • list_snapshots(): List all available snapshots with metadata
  • Detailed diff reports showing package, parameter, and data changes
  • Markdown report generation

Enhancements

• Updated DESCRIPTION with bioinformatics focus
• Enhanced documentation with bioinformatics examples
• Improved error handling and user feedback
• Better cross-platform compatibility
• Added utils to imports for better compatibility

Bug Fixes

• Fixed issue with checksum verification for legacy tracked files
• Improved handling of missing files in verification
• Better error messages for conda/mamba detection

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Capsule 0.1.0

Initial Release

Features

• Session Tracking: Comprehensive R session information capture

  • capture_session(): Capture R version, platform, and system info
  • capture_environment(): Capture global environment state

• Package Management: Complete package version tracking

  • snapshot_packages(): Create detailed package manifests
  • create_renv_lockfile(): Generate renv lockfiles
  • Automatic dependency graph creation

• Data Provenance: Track data files with integrity verification

  • track_data(): Record data source, checksums, and metadata
  • verify_data(): Verify data integrity via SHA-256 checksums
  • get_data_lineage(): Retrieve complete data provenance

• Parameter Tracking: Document analysis parameters

  • track_params(): Store analysis parameters with metadata
  • get_param_history(): Retrieve parameter history

• Random Seed Management: Reproducible random number generation

  • set_seed(): Set and track random seeds
  • restore_seed(): Restore previously tracked seeds
  • Complete RNG state tracking

• Script Generation: Create reproducible analysis scripts

  • generate_repro_script(): Generate executable R scripts
  • create_repro_report(): Generate markdown reports
  • Automatic integration of all tracked components

• Docker Support: Containerization for perfect reproducibility

  • generate_docker(): Generate Dockerfile and docker-compose.yml
  • RStudio Server support
  • Automatic system dependency configuration

• Workflow Management: Complete workflow orchestration

  • init_capsule(): Initialize Capsule in projects
  • snapshot_workflow(): Create complete workflow snapshots
  • Automatic artifact generation

Documentation

• Comprehensive README with quick start guide
• Complete function documentation with examples
• Example workflow demonstrating all features
• Docker usage instructions

Infrastructure

• MIT License
• Complete test suite
• Package structure following R best practices