nf-core/cnvflow: A Robust Nextflow Pipeline for Reproducible CNV Detection from Exome Data

Copy number variation (CNV) analysis plays a vital role in uncovering genomic alterations linked to disease. However, CNV detection workflows remain fragmented and often lack reproducibility. We present nf-core/cnvflow, a robust and reproducible Nextflow-based pipeline designed for read-depth-based CNV detection from exome data. The pipeline integrates four established CNV tools (CNVkit, CLAMMS, CoNIFER, and CONTRA) and supports containerized execution with Docker or Singularity. It accommodates diverse computing environments and includes automated quality control, coverage normalization, and tool-specific outputs. Benchmarking with 1000 Genomes Project data demonstrated its scalability and performance. nf-core/cnvflow provides a portable and extensible solution for standardized CNV analysis and is available under the nf-core community framework.