phylogenetic: Add config option to specify ancestral root sequence (#46)

Copied and modified from nextstrain/mpox@0bd64d3

Allow users to define an optional `--root-sequence` for `augur ancestral`

Adds in resolve_config path for nextstrain run support

Author: j23414

phylogenetic/defaults/config.yaml

@@ -25,6 +25,7 @@ refine:
 
 ancestral:
   inference: "joint"
+  root_sequence: "reference.gb"
 
 traits:
   north-america: country division MuV_genotype MuV_genotype_nextclade_sh MuV_genotype_nextclade_genome

phylogenetic/rules/annotate_phylogeny.smk

@@ -45,6 +45,11 @@ rule ancestral:
         "benchmarks/{build}/ancestral.txt",
     params:
         inference = config["ancestral"]["inference"],
+        root_sequence=lambda w: (
+            ("--root-sequence " + resolve_config_path(config["ancestral"]["root_sequence"])(w))
+            if config["ancestral"].get("root_sequence")
+            else ""
+        ),
     shell:
         r"""
         exec &> >(tee {log:q})
@@ -53,6 +58,7 @@ rule ancestral:
             --tree {input.tree:q} \
             --alignment {input.alignment:q} \
             --output-node-data {output.node_data:q} \
+            {params.root_sequence} \
             --inference {params.inference:q}
         """