Infer ancestral root

This commit reverts the change introduced in 9431655
which set the REFSEQ references as the roots in the auspice trees.
Turns out this is not the desired behavior for the dengue phylogenetic trees.

Instead, we want to use the sequences and metadata to infer the ancestral
root of each tree. These inferred-ancestral roots will then be used in building
the nextclade datasets as hard-coded reference and root of the scaffold trees.

phylogenetic/rules/annotate_phylogeny.smk

@@ -26,7 +26,6 @@ rule ancestral:
     input:
         tree = "results/{gene}/tree_{serotype}.nwk",
         alignment = "results/{gene}/aligned_{serotype}.fasta",
-        root_sequence = lambda wildcard: "config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb",
     output:
         node_data = "results/{gene}/nt-muts_{serotype}.json"
     params:
@@ -37,7 +36,6 @@ rule ancestral:
             --tree {input.tree} \
             --alignment {input.alignment} \
             --output-node-data {output.node_data} \
-            --root-sequence {input.root_sequence} \
             --inference {params.inference}
         """