Merge pull request #72 from nextstrain/default-tip-label

Default tip label

phylogenetic/defaults/auspice_config.json

@@ -1,56 +1,60 @@
-{
-  "title": "Real-time tracking of Zika virus evolution",
-  "maintainers": [
-    {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}
-  ],
-  "data_provenance": [
-    {
-      "name": "GenBank",
-      "url": "https://www.ncbi.nlm.nih.gov/genbank/"
-    },
-    {
-      "name": "USVI",
-      "url": "https://github.com/blab/zika-usvi/"
-    }
-  ],
-  "build_url": "https://github.com/nextstrain/zika",
-  "colorings": [
-    {
-      "key": "gt",
-      "title": "genotype",
-      "type": "categorical"
-    },
-    {
-      "key": "num_date",
-      "title": "date",
-      "type": "continuous"
-    },
-    {
-      "key": "author",
-      "title": "author",
-      "type": "categorical"
-    },
-    {
-      "key": "country",
-      "title": "country",
-      "type": "categorical"
-    },
-    {
-      "key": "region",
-      "title": "region",
-      "type": "categorical"
-    }
-  ],
-  "geo_resolutions": [
-    "country",
-    "region"
-  ],
-  "display_defaults": {
-    "map_triplicate": true
-  },
-  "filters": [
-    "country",
-    "region",
-    "author"
-  ]
-}
+{
+  "title": "Real-time tracking of Zika virus evolution",
+  "maintainers": [
+    {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}
+  ],
+  "data_provenance": [
+    {
+      "name": "GenBank",
+      "url": "https://www.ncbi.nlm.nih.gov/genbank/"
+    },
+    {
+      "name": "USVI",
+      "url": "https://github.com/blab/zika-usvi/"
+    }
+  ],
+  "build_url": "https://github.com/nextstrain/zika",
+  "colorings": [
+    {
+      "key": "gt",
+      "title": "genotype",
+      "type": "categorical"
+    },
+    {
+      "key": "num_date",
+      "title": "date",
+      "type": "continuous"
+    },
+    {
+      "key": "author",
+      "title": "author",
+      "type": "categorical"
+    },
+    {
+      "key": "country",
+      "title": "country",
+      "type": "categorical"
+    },
+    {
+      "key": "region",
+      "title": "region",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "country",
+    "region"
+  ],
+  "display_defaults": {
+    "map_triplicate": true,
+    "tip_label": "strain"
+  },
+  "metadata_columns": [
+    "strain"
+  ],
+  "filters": [
+    "country",
+    "region",
+    "author"
+  ]
+}

phylogenetic/defaults/config_zika.yaml

@@ -4,7 +4,6 @@ sequences_url: "https://data.nextstrain.org/files/workflows/zika/sequences.fasta
 metadata_url: "https://data.nextstrain.org/files/workflows/zika/metadata.tsv.zst"
 
 strain_id_field: "accession"
-display_strain_field: "strain"
 
 filter:
   group_by: "country year month"

phylogenetic/rules/export.smk

@@ -38,7 +38,7 @@ rule export:
         auspice_config = "defaults/auspice_config.json",
         description = "defaults/description.md"
     output:
-        auspice_json = "results/raw_zika.json"
+        auspice_json = "auspice/zika.json"
     params:
         strain_id = config.get("strain_id_field", "strain"),
     shell:
@@ -54,22 +54,3 @@ rule export:
             --include-root-sequence-inline \
             --output {output.auspice_json}
         """
-
-rule final_strain_name:
-    input:
-        auspice_json="results/raw_zika.json",
-        metadata="data/metadata_all.tsv"
-    output:
-        auspice_json="auspice/zika.json"
-    params:
-        strain_id=config["strain_id_field"],
-        display_strain_field=config.get("display_strain_field", "strain"),
-    shell:
-        """
-        python3 scripts/set_final_strain_name.py \
-            --metadata {input.metadata} \
-            --metadata-id-columns {params.strain_id} \
-            --input-auspice-json {input.auspice_json} \
-            --display-strain-name {params.display_strain_field} \
-            --output {output.auspice_json}
-        """