NEWS.md

In Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

Capsule 0.2.0

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

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

Capsule documentation built on Nov. 11, 2025, 5:14 p.m.