The advancement of digitalization in manufacturing has brought about a significant transformation in the industry. The digital thread, a key component this for transformation is defined as the use of digital tools and representations for design, evaluation, and life cycle management. This paper presents a project focused on enhancing the digital thread of a manufacturing line by integrating Model-Based Systems Engineering (MBSE) and Capella. It automates part identification, handling, and transportation in a small-scale manufacturing line, utilizing data from programs like Siemens NX in Capella to generate assembly code for manufacturing. The integration of various software tools like Capella, Siemens NX, and Mechatronics Concept Designer (MCD), along with hardware components like robots and Automated Guided Vehicles (AGVs), is crucial for optimizing manufacturing processes. The physical key components include cameras, sensors, and the UR10 robotic arm, demonstrating a use case of a flexible transport system (FTS) with a gripper and conveyor belt for pick-and-place tasks. The anticipated outcome is improved communication in the digital thread and increased production efficiency through automated processes, reduced manual intervention, and a more agile response to design changes.