Export strain, division and location as additional metadata

This swap to using --metadata-columns in augur export to surface strain, division and location.
nextstrain · Apr 12, 2024 · b51ea60 · b51ea60
1 parent 796f747
commit b51ea60
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Showing 4 changed files with 7 additions and 15 deletions.
diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json
@@ -25,11 +25,6 @@
       "key": "region",
       "title": "Region",
       "type": "categorical"
-    },
-    {
-      "key": "strain",
-      "title": "Strain name",
-      "type": "categorical"
     }
   ],
   "geo_resolutions": [

diff --git a/phylogenetic/defaults/auspice_config_N450.json b/phylogenetic/defaults/auspice_config_N450.json
@@ -25,12 +25,7 @@
       "key": "region",
       "title": "Region",
       "type": "categorical"
-    },
-    {
-      "key": "strain",
-      "title": "Strain name",
-      "type": "categorical"
-    }    
+    }
   ],
   "geo_resolutions": [
     "country",

diff --git a/phylogenetic/defaults/config.yaml b/phylogenetic/defaults/config.yaml
@@ -20,6 +20,8 @@ filter_N450:
 refine:
     coalescent: "opt"
     date_inference: "marginal"
-    clock_filter_iqd: 4  
+    clock_filter_iqd: 4
 ancestral:
     inference: "joint"
+export:
+    metadata_columns: "strain division location"
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -15,12 +15,12 @@ rule export:
         aa_muts = "results/{gene}/aa_muts.json",
         colors = config["files"]["colors"],
         auspice_config = lambda wildcard: "defaults/auspice_config.json" if wildcard.gene in ["genome"] else "defaults/auspice_config_N450.json"
-
     output:
         auspice_json = "auspice/measles_{gene}.json",
         root_sequence = "auspice/measles_{gene}_root-sequence.json"
     params:
-        strain_id = config["strain_id_field"]
+        strain_id = config["strain_id_field"],
+        metadata_columns = config["export"]["metadata_columns"]
     shell:
         """
         augur export v2 \
@@ -29,8 +29,8 @@ rule export:
             --metadata-id-columns {params.strain_id} \
             --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \
             --colors {input.colors} \
+            --metadata-columns {params.metadata_columns} \
             --auspice-config {input.auspice_config} \
             --include-root-sequence \
             --output {output.auspice_json}
         """
-