--reference is inputted by the user and also needs to be converted to an internal ID then
--root same
trees are plotted in the middle of the pipeline, so either plot them again at the final end or (better) replace IDs during the plotting process and also plot out final PNGs, PDFs, and SVGs for the HTML
At the moment a script checks for some dangerous symbols in FASTA headers.
It would be more convenient to initially rename the FASTA headers and then restore them at the final end of the pipeline. For example by using a python script: https://github.com/hoelzer/virify/blob/master/bin/rename_fasta.py
But there are some stumbling blocks:
--referenceis inputted by the user and also needs to be converted to an internal ID then--rootsame