This is a fork from jrflab/modules, specifically tailored and optimized for Whole Genome Sequencing (WGS) analysis. The pipeline includes enhanced resource allocation, WGS-specific tools, and comprehensive documentation.

git clone https://github.com/ipstone/modules.git
cd modules
git checkout master  # Default branch
./init_project

git clone https://github.com/ipstone/modules.git
cd modules  
git checkout mouse_wgs
./init_project

git clone https://github.com/ipstone/modules.git
cd modules
git checkout mouse
./init_project

After cloning, initialize a new project:

./modules/init_project
# or
perl modules/scripts/initProject.pl

• Documentation
• Module Documentation (master branch)
• Configuration Examples (master branch)

• GNU Make 3.82 or newer is required
• Cluster environment with SGE/PBS/LSF support (recommended)
• Conda environments for tool dependencies (see config.inc)

For issues specific to WGS optimizations or ipstone modifications, please contact the development team. For general jrflab/modules issues, refer to the original repository.

This repository maintains several specialized branches for different analysis scenarios:

• Purpose: Production-ready WGS analysis with latest updates
• Features:
  • WGS-optimized resource allocation (20G Picard memory, enhanced threading)
  • MIMSI analysis for microsatellite instability detection
  • Comprehensive documentation in _docs/ directory
  • GNU Make 3.82 compatibility
• Last Updated: 2025-07-12
• Use Case: Primary branch for human WGS projects

• Purpose: Historical merge point of jrflab updates into ipstone
• Features:
  • Integration of jrflab modules while preserving WGS optimizations
  • Updated genome references (dmp/current WGS reference)
• Date: 2019-08-16
• Use Case: Reference for understanding jrflab integration history

• Purpose: Mouse genome analysis (exome/targeted sequencing)
• Features:
  • Mouse reference genome (mm10) configuration
  • Deletion microhomology analysis adapted for mouse
• Date: 2020-02-28
• Use Case: Mouse exome sequencing projects

• Purpose: Mouse whole genome sequencing analysis
• Features:
  • Mouse WGS pipeline modifications
  • Enhanced memory specifications for somatic indel analysis
  • YAML loader parameter fixes
  • 12+ commits of mouse-specific optimizations
• Last Updated: 2025-03-06
• Use Case: Mouse WGS projects

• Purpose: Testing and validation branch
• Features:
  • Test cases for variant classification
  • Pathogenicity prediction validation
  • Sample test outputs
• Date: 2017-07-26
• Use Case: Development testing and validation