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

<h4>Motivation</h4>Antimicrobial resistance surveillance in ESKAPEE pathogens (<i>Enterococcus faecium</i>, <i>Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, <i>Enterobacter</i> spp., and <i>Escherichia coli</i>) 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.<h4>Results</h4>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 <i>K. pneumoniae</i> to <i>Enterobacter cloacae</i> sequence type 182), while confirming lineage assignments such as <i>E. coli</i> sequence type 131.<h4>Availability and implementation</h4>https://github.com/gmboowa/rMAP-2.0 and example workflow reports are available at: https://gmboowa.github.io/rMAP-2.0/.