Merge pull request #630 from nextstrain/remove-use-nextalign

Include distances and explicit aa muts by default
nextstrain · May 12, 2021 · d73ca13 · d73ca13
2 parents 41f24ad + 165fe31
commit d73ca13
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diff --git a/docs/change_log.md b/docs/change_log.md
@@ -5,6 +5,7 @@ We also use this change log to document new features that maintain backward comp
 
 ## New features since last version update
 
+ - 12 May 2021: Include S1 mutations and nextalign-based ancestral amino acid mutations in Auspice JSONs by default instead of requiring the now-unnecessary `use_nextalign` configuration parameter. ([#630](https://github.com/nextstrain/ncov/pull/630))
  - 12 May 2021: [Document all available workflow configuration parameters](https://nextstrain.github.io/ncov/configuration). ([#633](https://github.com/nextstrain/ncov/pull/633))
 
 ## v5 (7 May 2021)

diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
@@ -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)