The goal of this project is to develop standardized and reproducible workflows that can be applied in both research and clinical settings. Our focus is on clinically important viruses, including Human Immunodeficiency Virus (HIV), Enteroviruses, Hepatitis B/C/D viruses, Herpes Simplex Virus type 1 (HSV-1), and Cytomegalovirus (CMV). To analyze viral sequencing data, the workflows employ Nextflow (https://www.nextflow.io/), a domain-specific language (DSL) designed for scalable and parallelized computational pipelines. Using Nextflow, we automate key steps such as quality control, assembly, variant calling, consensus sequence generation, and resistance profiling. In line with best practices, the workflows will adhere to the FAIR principles (Findability, Accessibility, Interoperability, and Reusability of digital assets). To ensure long-term usability and sustainability, we are integrating these workflows into the nf-core/viralrecon framework (https://github.com/nf-core/viralrecon). The nf-core community develops pipelines that follow clear standards for reproducibility, portability, and robustness, making them widely adoptable across institutions. However, developing and testing these pipelines requires more computing power than our local machines can provide. Limited CPU and memory resources make it challenging to test efficiently and slow down the development process. High-performance computing (HPC) resources are therefore essential, as they allow us to run multiple workflow steps in parallel. The requested HPC resources will be dedicated to development and testing. We do not plan to conduct large-scale production analyses on the cluster, but rather to optimize and validate the workflows prior to broader implementation. In summary, access to HPC resources will enable us to overcome local hardware constraints, accelerate pipeline development, and ensure the delivery of robust workflows. Ultimately, these workflows will enhance viral genotyping and resistance testing, providing significant benefits for both research and clinical applications.