Look at the FDA testing protocol [1] for their Covid-19 test kit.
They use molecular water (double-distilled, deionized, likely de-salted water), and DNA and RNA degradation solutions, some PPE, autoclaves, bleach, and lots of workflow procedures to carefully mitigate cross-contamination.
I'm curious why the life sciences folks aren't standardized upon something like semiconductor SMIF to isolate the samples and point of contact of equipment into a modular sterile environment, and limit cleaning to interface ports optimized for sterile operations and maintenance. My first swag at such interface ports might look into some design that can be clamped and autoclaved, and submerged in some degradation solution, for example. Generally, the current open standard is terrifically manual labor intensive and prone to mistakes.
All the automated solutions I've been able to read up on so far (BD MAX, Seegene All-In-One Platform, Roche Cobas 6600/8800, BioFire FilmArray Torch and FilmArray 2.0) seem to lock in customers to proprietary panels. I'm curious whether that is more of a commercial decision or a scientific decision. Of these, only BD MAX allows user-designed protocols at all.
So far, I've yet to see a persuasive argument that an automated molecular diagnostics system must use a proprietary platform for scientific reasons. A generic automated platform that can use anyone's glassware, molecular water, primers, master mixes, etc., will need many more sensors for quality monitoring, and those need constant calibration, so there is a significant engineering tradeoff. But I'd be surprised if any of the proprietary solutions are much more cost-effective; it seems all of these kinds of solutions are following the John Deere lock-in servicing model to generate profits.
[1] https://www.fda.gov/media/134922/download