Include distances and explicit aa muts by default
We used to only include these annotations in auspice JSONs when
`use_nextalign` was set to `true`. Now that nextalign is the
default (and only) aligner, we should always include these annotations
and allow users who never enabled nextalign to benefit from them.
@@ -1128,12 +1128,11 @@ def _get_node_data_by_wildcards(wildcards):
rules.clades.output.clade_data,
rules.recency.output.node_data,
rules.traits.output.node_data,
- rules.logistic_growth.output.node_data
+ rules.logistic_growth.output.node_data,
+ rules.aa_muts_explicit.output.node_data,
+ rules.distances.output.node_data
]
- if "use_nextalign" in config and config["use_nextalign"]:
- inputs.append(rules.aa_muts_explicit.output.node_data)
- inputs.append(rules.distances.output.node_data)
if "run_pangolin" in config and config["run_pangolin"]:
inputs.append(rules.make_pangolin_node_data.output.node_data)
