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

## TL;DR

rMAP 2.0 is a flexible and reproducible workflow for analyzing genomes of drug-resistant bacteria, designed to work offline or in the cloud.

## Contribution

rMAP 2.0 introduces a containerized genomic analysis pipeline for ESKAPEE pathogens that supports offline execution and consistent results across platforms.

## Key findings

- rMAP 2.0 processed 20 Enterobacterales isolates in ~4.5 hours on a laptop.
- The workflow identified a misannotated public genomic record (SRR9703249).
- It confirmed lineage assignments like E. coli sequence type 131.

## Abstract

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.

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.

https://github.com/gmboowa/rMAP-2.0 and example workflow reports are available at: https://gmboowa.github.io/rMAP-2.0/