Phylogenetic placement part 2

[erikrikarddaniel]

Description of feature

If --pplace or not --skip_pplace run phylogenetic placement with standard data.

Add reference data to taxonomy reference configs so that:

Accept a list of taxa in the form of d__Bacteria pointing to ref tree, alignment, model, align method and name. Grep output taxonomy assignment with the keys and subset ASV sequences for each tree/alignment etc.

In a separate config context:

[
  d__Bacteria = [
    alignmethod: "mafft",
    refseqfile: "_url_",
    refphylogeny: "_url_",
    reftaxonomy: "_url_",
    model: "GTR+I",
    pplace_name: "GTDB Bacteria"
  ],
  d__Archaea = [
    ...
  ]
]