Use new augur ancestral interface

Updates augur ancestral rule in the core workflow to generate ancestral
translations in addition to ancestral nucleotide sequences. Removes the
separate rule for translation and the corresponding custom script.
Updates all downstream rules to reference a new single `muts.json` file.
Rules that depended on the translations with internal node sequences do
not need to change, since the output files from the updated ancestral
rule maintain the same name.

workflow/snakemake_rules/core.smk

@@ -266,12 +266,19 @@ rule refine:
 rule ancestral:
     message: "Reconstructing ancestral sequences and mutations"
     input:
-        tree = rules.refine.output.tree,
-        alignment = rules.align.output.alignment,
+        tree = build_dir + "/{build_name}/{segment}/tree.nwk",
+        alignment = build_dir + "/{build_name}/{segment}/aligned.fasta",
+        translations = aggregate_translations,
+        reference =  lambda w: f"{config['builds'][w.build_name]['reference']}",
+        annotation = lambda w: f"{config['builds'][w.build_name]['annotation']}",
     output:
-        node_data = build_dir + "/{build_name}/{segment}/nt-muts.json"
+        node_data = build_dir + "/{build_name}/{segment}/muts.json",
+        translations_done = build_dir + "/{build_name}/{segment}/translations.done",
     params:
-        inference = "joint"
+        inference = "joint",
+        genes = lambda w: GENES[w.segment],
+        input_translations = lambda w: build_dir + f"/{w.build_name}/{w.segment}/nextalign/masked.gene.%GENE.fasta",
+        output_translations = lambda w: build_dir + f"/{w.build_name}/{w.segment}/nextalign/masked.gene.%GENE_withInternalNodes.fasta",
     conda: "../envs/nextstrain.yaml"
     benchmark:
         "benchmarks/ancestral_{build_name}_{segment}.txt"
@@ -284,36 +291,13 @@ rule ancestral:
         augur ancestral \
             --tree {input.tree} \
             --alignment {input.alignment} \
-            --output-node-data {output.node_data} \
-            --inference {params.inference} 2>&1 | tee {log}
-        """
-
-rule translate:
-    message: "Translating amino acid sequences"
-    input:
-        translations = aggregate_translations,
-        tree = rules.refine.output.tree,
-        reference =  lambda w: f"{config['builds'][w.build_name]['reference']}",
-        annotation = lambda w: f"{config['builds'][w.build_name]['annotation']}",
-    output:
-        node_data = build_dir + "/{build_name}/{segment}/aa_muts.json",
-        translations_done = build_dir + "/{build_name}/{segment}/translations.done"
-    params:
-        genes = lambda w: GENES[w.segment]
-    conda: "../envs/nextstrain.yaml"
-    benchmark:
-        "benchmarks/translate_{build_name}_{segment}.txt"
-    log:
-        "logs/translate_{build_name}_{segment}.txt"
-    shell:
-        """
-        python3 scripts/translations_aamuts.py \
-            --tree {input.tree} \
+            --root-sequence {input.reference} \
             --annotation {input.annotation} \
-            --reference {input.reference} \
-            --translations {input.translations:q} \
             --genes {params.genes} \
-            --output {output.node_data} 2>&1 | tee {log} && touch {output.translations_done}
+            --translations "{params.input_translations}" \
+            --output-node-data {output.node_data} \
+            --output-translations "{params.output_translations}" \
+            --inference {params.inference} 2>&1 | tee {log} && touch {output.translations_done}
         """
 
 rule traits:
@@ -347,8 +331,7 @@ rule traits:
 rule clades:
     input:
         tree = build_dir + "/{build_name}/ha/tree.nwk",
-        nt_muts = build_dir + "/{build_name}/ha/nt-muts.json",
-        aa_muts = build_dir + "/{build_name}/ha/aa_muts.json",
+        muts = build_dir + "/{build_name}/ha/muts.json",
         clades = lambda wildcards: config["builds"][wildcards.build_name]["clades"],
     output:
         node_data = build_dir + "/{build_name}/ha/clades.json",
@@ -361,7 +344,7 @@ rule clades:
         """
         augur clades \
             --tree {input.tree} \
-            --mutations {input.nt_muts} {input.aa_muts} \
+            --mutations {input.muts} \
             --clades {input.clades} \
             --output {output.node_data} 2>&1 | tee {log}
         """
@@ -370,8 +353,7 @@ rule clades:
 rule subclades:
     input:
         tree = build_dir + "/{build_name}/{segment}/tree.nwk",
-        nt_muts = build_dir + "/{build_name}/{segment}/nt-muts.json",
-        aa_muts = build_dir + "/{build_name}/{segment}/aa_muts.json",
+        muts = build_dir + "/{build_name}/{segment}/muts.json",
         clades = lambda wildcards: config["builds"][wildcards.build_name]["subclades"],
     output:
         node_data = build_dir + "/{build_name}/{segment}/subclades.json",
@@ -387,7 +369,7 @@ rule subclades:
         """
         augur clades \
             --tree {input.tree} \
-            --mutations {input.nt_muts} {input.aa_muts} \
+            --mutations {input.muts} \
             --clades {input.clades} \
             --membership-name {params.membership_name} \
             --label-name {params.label_name} \
@@ -398,8 +380,7 @@ rule subclades:
 rule import_clades:
     input:
         tree = build_dir + "/{build_name}/ha/tree.nwk",
-        nt_muts = build_dir + "/{build_name}/{segment}/nt-muts.json",
-        aa_muts = build_dir + "/{build_name}/{segment}/aa_muts.json",
+        muts = build_dir + "/{build_name}/{segment}/muts.json",
         clades = build_dir + "/{build_name}/ha/clades.json",
     output:
         node_data = build_dir + "/{build_name}/{segment}/clades.json",

workflow/snakemake_rules/export.smk

@@ -8,7 +8,6 @@ def _get_node_data_by_wildcards(wildcards):
     inputs = [
         rules.refine.output.node_data,
         rules.ancestral.output.node_data,
-        rules.translate.output.node_data,
         rules.clades.output.node_data,
         rules.traits.output.node_data,
         rules.annotate_epiweeks.output.node_data,