EURYALE: A versatile Nextflow pipeline for taxonomic classification and functional annotation of metagenomics data

EURYALE is a Nextflow pipeline designed for the sensitive taxonomic classification and flexible functional annotation of metagenomic shotgun sequences. It provides a comprehensive solution for preprocessing, assembly, alignment, taxonomic classification, and functional annotation of metagenomic data. EURYALE builds upon the Snakemake-based pipeline MEDUSA. EURYALE inherits the tools present in MEDUSA, selected based on rigorous benchmarks for performance, accuracy, and sensitivity. The new pipeline has been developed with the nf-core pipeline template, which focuses on modularity, allowing a high degree of parameterization. EURYALE provides easier resource management, enforcing strict memory and CPU requirements based on its Nextflow configuration. It has also become more versatile, as it can be executed using Docker and Singularity, which further extends its usability across various platforms. It can also natively take advantage of computational infrastructures such as SLURM and Amazon Web Services. EURYALE inherits the sensitivity in taxonomic classification and flexibility in functional annotation of its predecessor, combined with improved versatility.