A robust, Dockerized WDL/Cromwell workflow for Mycobacterium tuberculosis complex genomic surveillance, integrating read trimming, QC, species typing, TB-Profiler resistance & lineage profiling, NTM/MTBC identification, mutation evidence reporting, core-SNP phylogenomics, SNP distance analysis & interactive HTML reporting for TB AMR surveillance.

WGS-based drug resistance profiling and lineage classification of 15 Mycobacterium tuberculosis isolates from South Africa using TB-Profiler and Python.