I’m new to the field of phylogenetics/genomics but my lab has tasked me with assembling genomes of bioprospected organisms and performing a phylogenetic analysis of them. Is nf-core/phyloplace a suitable pipeline to use for whole genome assemblies? If not, is there an alternative way to do phylogenetics when you have draft assemblies that’s more robust than 16/18s sequencing that anyone would recommend?

For whole genome assemblies you probably want to look at #CE9MS66BS

If you with "phylogenetic analysis" mean a de novo tree, phyloplace does not do that. It's for placing unknown individual sequences in trees that were already estimated. And even if you have reference tree, e.g. the GTDB tree, phyloplace lacks the capacity to search for marker genes, align them etc. that tools like GTDB-Tk does, so it's difficult to use it directly for phylogenetic placement of genomes. I would therefore recommend GTDB-Tk. This tool is built into #CE9MS66BS, so if you haven't already assembled and binned your genomes, I'd recommend that you use that pipeline for the whole analysis: assembly, binning, completeness/contamination analysis, taxonomy based on the GTDB phylogeny and functional annotation. If you have already done the assembly, binning etc. I recommend that you use GTDB-Tk directly.