We are excited to announce Version 3.0.0. In this release, a new Makefile has been introduced to streamline the execution of the entire analysis pipeline, featuring make all for running the full sequence and make clean for removing generated files. Code from existing scripts has been abstracted into reusable functions, stored in a new src directory, and accompanied by unit tests to enhance code reusability and ensure functionality. Additionally, significant improvements were made based on feedback received from earlier milestones and peer reviews, with detailed GitHub Issues documenting the changes. The project structure has been refined for better maintainability and clarity.