During their recent work on the EIT-Pathogena/client repository, Matthew Colpus focused on improving the reliability of pathogen decontamination workflows by addressing a critical bug related to Bowtie alignment consistency. By updating the decontaminate_samples_with_hostile function to always pass the --local argument to Bowtie, Matthew ensured that local and cloud-based processing would yield consistent results, reducing nondeterministic behavior and minimizing downstream debugging. This targeted fix, implemented using Python and leveraging command line interface skills within a bioinformatics context, enhanced the reproducibility and confidence in pipeline outputs. The work demonstrated careful attention to cross-environment parity and workflow robustness.