Bringing spatial omics to nf-core
Victor Perez, Florian Wünnemann, Denis Schapiro, Jeremy Muhlich, Artem Sokolov, Clarence Yapp, Jose Nimo, Miguel Ibarra Arellano, Margot Chazotte, Chiara Schiller, Aroj Hada, Krešimir Beštak, Wouter-Michiel Vierdag, and Adam Taylor
Novel spatial omics technologies enable measurements of various readouts (genomics, transcriptomics, proteomics, metabolomics,microbiome and more) with spatial resolution within intact tissue structures. This novel layer of information provides unprecedented insights into tissues in health and diseases. While nf-core currently hosts a large collection of omics pipelines, imaging and spatial analysis remain an unmet need. Our goal is to bring image analysis pipelines to the nf-core community. As a first step, we made the popular nextflow pipeline MCMICRO available in nf-core by converting most of the MCMICRO functionalities to DSL2 modules in nf-core. Here, we will present new workflows tailored to a collection of different spatial omics acquisition technologies. By creating a foundation of image analysis tools within nf-core, we aim to provide easy entry points for the spatial omics community.