Clinical-Genomics/microSALT ? reverse-engineered prompt

Build me a microbial sequence analysis pipeline that takes NGS whole genome data, checks sample quality, figures out the organism type and sequence type, and predicts resistance patterns. I want it to run jobs on a SLURM cluster, store results in a MySQL database, and generate clean HTML reports that can be emailed to the user when the run is done.

It should have a simple setup command that creates the needed database tables and downloads the reference data, plus a utility area for things like creating sample description files, adding new reference organisms, and regenerating reports. Use the right tools for the workflow, including report templates and container based analysis steps, and make sure it can work with common MLST and resistance gene databases. If you need current install or dependency details, look them up online and follow the project docs closely.