Merge pull request #180 from nextstrain/use-gisaid-epi-isl

Use `gisaid_epi_isl` in workflows
nextstrain · Oct 16, 2024 · 3b7ce7a · 3b7ce7a
2 parents da27f26 + 6ddfdba
commit 3b7ce7a
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Showing 12 changed files with 57 additions and 102 deletions.
diff --git a/config/h1n1pdm/auspice_config.json b/config/h1n1pdm/auspice_config.json
@@ -87,16 +87,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -164,5 +154,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json
@@ -162,16 +162,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -239,5 +229,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json
@@ -127,16 +127,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -204,5 +194,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/h3n2/auspice_config.json b/config/h3n2/auspice_config.json
@@ -97,16 +97,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -174,5 +164,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/h3n2/auspice_config_fitness.json b/config/h3n2/auspice_config_fitness.json
@@ -152,5 +152,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json
@@ -179,16 +179,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -256,5 +246,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json
@@ -112,16 +112,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -189,5 +179,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/vic/auspice_config.json b/config/vic/auspice_config.json
@@ -72,16 +72,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -149,5 +139,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json
@@ -119,16 +119,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -196,5 +186,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json
@@ -112,16 +112,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -189,5 +179,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/config/yam/auspice_config.json b/config/yam/auspice_config.json
@@ -67,16 +67,6 @@
       "title": "Division",
       "type": "categorical"
     },
-    {
-      "key": "accession_ha",
-      "title": "Accession (HA)",
-      "type": "categorical"
-    },
-    {
-      "key": "accession_na",
-      "title": "Accession (NA)",
-      "type": "categorical"
-    },
     {
       "key": "submitting_lab",
       "title": "Submitting lab",
@@ -127,5 +117,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_epi_isl",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/nextclade/Snakefile b/nextclade/Snakefile
@@ -410,8 +410,8 @@ rule export:
     output:
         auspice_json="build/{lineage}/{segment}/{reference}/auspice.json",
     params:
-        fields="strain region country date isolate_id accession_{segment}",
-        select_fields = ','.join(["strain", "region", "country", "date", "isolate_id", "accession_{segment}"]),
+        fields="strain region country date gisaid_epi_isl accession_{segment}",
+        select_fields = ','.join(["strain", "region", "country", "date", "gisaid_epi_isl", "accession_{segment}"]),
         date=datetime.datetime.utcnow().strftime("%Y-%m-%d"),
     shell:
         """