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Abstract The broadening utilisation of ancient DNA (aDNA) to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned pipeline for the analysis of ancient genomic data. nf-core/eager builds on existing ideas and concepts introduced in the original EAGER pipeline, and improves various aspects of the analysis procedure by employing computational frameworks such as Nextflow and nf-core. The pipeline aims to address three main themes: accessibility and adaptability to different research groups and their computing configurations, reproducibility to ensure robust analytical standards in the field, and updating the EAGER pipeline to the latest routine ancient genomic practises. This new version of EAGER has been developed within the nf-core initiative, to ensure high quality software development and maintenance support; contributing to a long-term lifecycle for the pipeline. nf-core/eager will assist in ensuring that ancient DNA sequencing data can be used by a diverse range of research groups and fields.