TaxoFlow: a step-by-step tutorial to build a nextflow pipeline for metagenomics taxonomic classification

Abstract

Reproducibility challenges scientific reporting, including metagenomics, where increasingly complex bioinformatics pipelines hinder transparency, comparability, and customization for life science students globally. To address this demanding task, we built an open, interactive and web-based tutorial that guides scholars with basic command-line skills through the detailed development of a validated and reproducible Nextflow metagenomics classification pipeline. As important features, the tutorial emphasizes simplicity, modularity, and containerization, which empowers users with both conceptual understanding and practical implementation skills. Noteworthy, this tutorial provides all the required files, databases, dependencies, software and environment for users to run it without the need of local installation or computational adaptations elsewhere. Finally, by offering a fully reproducible pipeline with a step-by-step developing tutorial, this work aims to lower technical barriers in microbiome bioinformatics and promote best practices in metagenomics data analysis. TaxoFlow is freely available at https://taxoflow.work/.