Feature request phylogenetic analysis subworkflow

[OmkarSaMo]

I think it would be valuable to create a phylogenetic tree sub workflow.

1. autoMLST-based tree
2. GTDB tree using de_novo_wf
3. Roary core genome alignment tree

Perhaps we can add a compare_phylo rule to compare if different trees are in agreement with each other.

We can consider other options too.

@drboothtj let us know your thoughts on this sub-workflow that can do different relevant phylogenetic analysis.

[drboothtj]

This is definitely doable!

We can add getphylo and I have already written scripts for comparing trees and alignments. With a little tweaking I could formalise these scripts to produce a nice report (the current output is just text lines).

We could also add IQ-TREE for hardcore phylogenetics runs. I'm not experienced writing workflows but I'd be happy to work together to get these added!

[matinnuhamunada]

This is now implemented in the PR for v0.7.9 as a BGC subworkflow