While diagnostics are critical for accurate and timely diagnosis, gold-standard diagnostic tests are commonly high- performance laboratory-based tests that require multi-step protocols for complex sample processing and highly trained personnel, both scarce in low-resource settings. Here, we address the need for an easy-to-use, rapid and reliable diagnostic testing pipeline by presenting a solution combining open-source modular automation and automation compatible microfluidics, easily adaptable to a pipeline for infectious diseases diagnosis. We demonstrate an automation compatible microfluidics pipeline for Neisseria meningitidis diagnosis by on-chip nucleic acids isolation and isothermal amplification, as well as pathogen detection on a paper-based microarray.