Metagenomics and, in particular, ancient metagenomics have become essential tools for reconstructing past ecosystems, tracking pathogen evolution, and characterizing microbial communities from environmental and archaeological samples. The aMeta pipeline (Pochon et al., 2023) is currently one of the most accurate workflows for authenticating ancient microbial DNA from shotgun sequencing data, combining taxonomic profiling (KrakenUniq), competitive mapping (Bowtie2/MALT), and authentication metrics (damage patterns, edit distance, breadth of coverage). However, aMeta is implemented in Snakemake, which limits its portability, scalability on heterogeneous HPC systems, and its ability to dynamically allocate resources per sample and per process. This project aims to convert, modernize, and expand the aMeta pipeline into a Nextflow DSL2 implementation, following nf-core community standards. Nextflow offers superior resource management, native container support (Singularity/Docker), dynamic retries with resource escalation, and seamless execution across SLURM-based HPC systems such as those provided by NAISS. The rewritten pipeline will improve throughput by parallelizing per-sample and per-reference computations, reducing wall-clock time on large cohorts, and by optimizing memory-intensive steps (KrakenUniq database loading, MALT alignment) through smarter job grouping and caching. The project has three main objectives: (1) reimplement all aMeta modules in Nextflow DSL2 with modular, testable processes; (2) benchmark the new pipeline against the original Snakemake implementation on real ancient DNA datasets (publicly available sedimentary and dental calculus samples from ENA/SRA) in terms of runtime, memory efficiency, and reproducibility of authentication results; and (3) extend the pipeline with additional functionality, including support for long-read data, improved damage-pattern statistics, expanded reference database management, and integrated MultiQC reporting. Development will involve iterative testing on subsets of publicly available ancient metagenomic datasets, followed by full-scale validation runs using the standard NCBI RefSeq microbial database and custom KrakenUniq/MALT databases (~500 GB–1 TB). The resulting pipeline will be released as open-source software and submitted for inclusion in nf-core, benefiting the international ancient DNA and metagenomics communities, and will serve as a foundation for future large-scale metagenomic studies in Sweden and abroad.