ViralFlow v1.0 is a computational workflow designed for viral genomic surveillance, offering a general-purpose reference-based genome assembler for all viruses with available reference genomes. Key improvements include the implementation of virus-agnostic modules for nucleotide and amino acid mutation analysis, enhanced modularity, and better management through the NextFlow workflow language. This version supports a wide range of computational infrastructures, from laptops to high-performance computing (HPC) environments, and generates well-formatted outputs suitable for public health reporting and scientific research. The workflow processes raw reads, performs quality control, aligns reads to a reference genome, and generates consensus genomes, mutation annotations, and visualization tools. Performance evaluations using simulated and real datasets demonstrate consistent results and improved scalability. ViralFlow v1.0 is available at <https://viralflow.github.io/index-en.html> and is publicly accessible on GitHub and Figshare.ViralFlow v1.0 is a computational workflow designed for viral genomic surveillance, offering a general-purpose reference-based genome assembler for all viruses with available reference genomes. Key improvements include the implementation of virus-agnostic modules for nucleotide and amino acid mutation analysis, enhanced modularity, and better management through the NextFlow workflow language. This version supports a wide range of computational infrastructures, from laptops to high-performance computing (HPC) environments, and generates well-formatted outputs suitable for public health reporting and scientific research. The workflow processes raw reads, performs quality control, aligns reads to a reference genome, and generates consensus genomes, mutation annotations, and visualization tools. Performance evaluations using simulated and real datasets demonstrate consistent results and improved scalability. ViralFlow v1.0 is available at <https://viralflow.github.io/index-en.html> and is publicly accessible on GitHub and Figshare.