Update summary scripts to deal with QIIME2 model changes

[cjfields]

Description of the bug

Recent outputs from the workflow, which has a feature branch updating to the latest QIIME2 release (2026.7) reveal issues with the outputs in both the R RDS taxonomic tables and the taxtab.txt outputs. This appears due to the inclusion of new ranks in the latest Silva 144 release (see the additional k__ column).

The most robust solution would be to autodetect ranks where possible, falling back to user-derived ranks if given (and exiting loudly if there is a mismatch on matrix dimensions).

"#OTU ID"       "Domain"        "Phylum"        "Class" "Order" "Family"        "Genus" "Species"
"9bd6b38174be13bed4d2888dd7a8839d"      "d__Bacteria"   "k__Pseudomonadati"     "p__Pseudomonadota"     "c__Alphaproteobacteria"        "o__Rickettsiales"      "f__Ehrlichiaceae"
      "g__Candidatus_Neowolbachia"
"945184b6386c192c0066e0a98a154780"      "d__Bacteria"   "k__Pseudomonadati"     "p__Pseudomonadota"     "c__Gammaproteobacteria"        "o__Enterobacterales"   "f__Enterobacteriaceae" NA
"636b2ba0cb950a596c5037a996efe675"      "d__Bacteria"   "k__Pseudomonadati--other"      "p__Spirochaetota"      "c__Spirochaetia"       "o__Spirochaetales"     "f__Spirochaetaceae--other"     "g__Entomospira"
...

### Command used and terminal output

```console

Relevant files

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System information

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