[TheiaProk] Add QC threshold functionality to export_taxon_tables optional task

[kapsakcj]

🆒

📌 Explain the Request

A user requested that they wanted to mirror the functionality of BioNumerics/PulseNet 2.0 in the ability to separate out WGS results based on taxon (E. coli/Shigella, Salmonella, Campylobacter, etc.) AND based on QC pass or fail status.

We currently have functionality to export TheiaProk results to additional Terra data tables (e.g. salmonella_specimen data table with all Salmonella samples) based on GAMBIT taxonomic prediction, but there is no functionality to filter out samples that do not pass QC.

This development effort may require altering the way that the optional qc_check task is performed and it's outputs. I think it currently creates "warnings" or "QC_ALERT" messages, but doesn't outright "fail" sample based on the thresholds set in the qc_check input TSV. We may have to adjust the qc_check outputs and perhaps standardize QC thresholds for various organisms to make this work properly.

All ideas welcome here, this is not a fully thought-out feature request yet.