Genetic analysis of molecular traits such as gene expression, splicing and chromatin accessibility requires a number of complex analysis steps that can easily take weeks or months for a analyst to implement from scratch. In the CINECA project, we have developed a number of modular Nextflow workflows that standardise and automate these steps. In this webinar, we will give an overview of the CINECA workflows for genotype imputation, gene expression and splicing quantification, data normalisation and association testing, and demonstrate how these workflows can be used in a federated setting without transferring identifiable personal data between partners.