rMAP 2.0: a modular, reproducible, and scalable WDL–Cromwell–Docker workflow for genomic analysis of ESKAPEE pathogens

Abstract Motivation Antimicrobial resistance surveillance in ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) requires reproducible, portable whole-genome analysis that public health laboratories including those operating under data-sovereignty constraints can run on laptops, institutional servers, or cloud backends without local dependency conflicts. rMAP 2.0 addresses these needs using a containerized Workflow Description Language pipeline executed with Cromwell. Results rMAP 2.0 standardizes end-to-end bacterial whole-genome analysis—read quality control, trimming, assembly and annotation, resistance/virulence/mobile-element profiling, sequence typing, pangenome inference, and phylogenetic reconstruction using containerized execution, and generates a single interactive HTML report that collates outputs for rapid review. The workflow supports fully offline execution (including BLAST searches) for data-sovereign deployments and can run on local workstations, institutional servers, and cloud backends where Docker is supported, providing a consistent execution environment without local tool installation. In a representative benchmark of 20 Enterobacterales isolates, rMAP 2.0 completed a cohort run in ∼4.5 hours on an 8-core/16-GB laptop and flagged a public record misannotated in public repository metadata (SRR9703249, reclassified from K. pneumoniae to Enterobacter cloacae sequence type 182), while confirming lineage assignments such as E. coli sequence type 131. Availability and implementation https://github.com/gmboowa/rMAP-2.0 and example workflow reports are available at: https://gmboowa.github.io/rMAP-2.0/