Merge pull request #154 from nextstrain/download-clades

Download clade definitions from GitHub

Snakefile

@@ -20,6 +20,33 @@ lineage_name_by_abbreviation = {
     "yam": "Yam",
 }
 
+clade_url_by_lineage_and_segment = {
+    "h1n1pdm": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/main/.auto-generated/clades.tsv",
+    },
+    "h3n2": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/main/.auto-generated/clades.tsv",
+    },
+    "vic": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_HA/main/.auto-generated/clades.tsv",
+    }
+}
+
+subclade_url_by_lineage_and_segment = {
+    "h1n1pdm": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/main/.auto-generated/subclades.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_NA/main/.auto-generated/subclades.tsv",
+    },
+    "h3n2": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/main/.auto-generated/subclades.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/main/.auto-generated/subclades.tsv",
+    },
+    "vic": {
+        "ha": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_HA/main/.auto-generated/subclades.tsv",
+        "na": "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_B-Vic_NA/main/.auto-generated/subclades.tsv",
+    }
+}
+
 if "data_source" in config and config["data_source"]=='fauna':
     include: "workflow/snakemake_rules/download_from_fauna.smk"