v0.3.0

This release renames the Apollo_Illumina_PE workflow to TheiaProk_Illumina_PE workflow restructures the PHBG task directory

The TheiaProk workflow was developed to replace Apollo workflows for bacterial genomic characterization. TheiaProk is based off of @rpetit3's Bactopia and its Merlin subworkflow and differs from the original Apollo workflows in its organism-typing subworkflow merlin_magic.

This subworkflow triggers organism typing based on gambit taxon assignments for each sample, e.g. serotyping via SeroTypeFinder will be performed for samples with an Escherichia gambit taxon assignment.

TheiaProk organism typing will be performed for the following organisms using the listed bioinformatics software:

• Eschericia spp.: serotypefinder & ectyper
• Listeria spp.: lissero
• Salmonella spp.: sistr & seqsero2
• Klebsiella spp.: kleborate
• Mycobacterium spp.: tbprofiler

TheiaProk_Illumina_PE will also perform AMR gene detection using abricate against the NCBI AMRFinderPlus database.

Additionally, the PHBG directory structure was reformatted for ease of use and readability.