Inferring and evaluating network medicine-based disease modules with nextflow

Motivation: Most diseases result from complex molecular interactions of genes and proteins. Various network-based methods characterize these mechanisms by expanding seed genes into disease modules. Their underlying algorithmic strategies differ, making it difficult to determine which of the created modules are most useful or biologically plausible. Results: To address this challenge, we developed an all-in-one pipeline that handles installation, input preparation, execution, and systematic evaluation of six widely used module detection tools, considering module topology, functional coherence, robustness, and the capacity to recover seeds. To showcase the value of our pipeline and provide guidance to potential users, we conducted a comprehensive evaluation across 50 different disease-network combinations, revealing substantial variability among the derived disease modules, driven by both network and algorithm choices. We show that methods are robust to minor perturbations but struggle to recover omitted seeds. None consistently outperforms all others, underscoring the need for careful method selection. Our work enables the systematic comparison of disease module discovery approaches and promotes reproducible network medicine research. Integrated into the nf-core project, it is intended as an extendable, long-term resource for tracking progress in the field. Availability and Implementation: The pipeline is implemented in Nextflow. Code and documentation are available through GitHub (https://github.com/nf-core/diseasemodulediscovery) and the nf-core website (https://nf-co.re/diseasemodulediscovery). Code and data used for demonstrating the pipeline are available through GitHub (https://github.com/REPO4EU/modulediscovery_demonstration).