WIP: collection of change will fix later

nextstrain · Jan 24, 2025 · cbd0616 · cbd0616
1 parent 19f50ac
commit cbd0616
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Showing 3 changed files with 25 additions and 1 deletion.
diff --git a/phylogenetic/defaults/clades.tsv b/phylogenetic/defaults/clades.tsv
@@ -0,0 +1,5 @@
+# Define clade-defining mutations
+clade	gene	site	alt
+SW3	NS4A	85	T
+SW3	NS5	314	R
+WN02	E	159	A
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
@@ -96,3 +96,21 @@ rule traits:
             --columns {params.metadata_columns:q} \
             --confidence 2>&1 | tee {log}
         """
+
+rule clades:
+    """Annotating serotypes / genotypes"""
+    input:
+        tree = "results/{build}/tree.nwk",
+        nt_muts = "results/{build}/nt_muts.json",
+        aa_muts = "results/{build}/aa_muts.json",
+        clade_defs = "defaults/clades.tsv",
+    output:
+        clades = "results/{build}/clades.json"
+    shell:
+        """
+        augur clades \
+            --tree {input.tree} \
+            --mutations {input.nt_muts} {input.aa_muts} \
+            --clades {input.clade_defs} \
+            --output {output.clades}
+        """
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -34,6 +34,7 @@ rule export:
         traits = "results/{build}/traits.json",
         nt_muts = "results/{build}/nt_muts.json",
         aa_muts = "results/{build}/aa_muts.json",
+        clades = "results/{build}/clades.json",
         description = config["export"]["description"],
         auspice_config = config["export"]["auspice_config"],
     output:
@@ -48,7 +49,7 @@ rule export:
             --tree {input.tree} \
             --metadata {input.metadata} \
             --metadata-id-columns "accession" \
-            --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
+            --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} {input.clades} \
             --description {input.description} \
             --auspice-config {input.auspice_config} \
             --include-root-sequence-inline \