nextclade: add dataset shortcuts

nextstrain · Jan 9, 2024 · 0c05325 · 0c05325
1 parent f8b5493
commit 0c05325
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Showing 3 changed files with 15 additions and 1 deletion.
diff --git a/nextclade/Snakefile b/nextclade/Snakefile
@@ -257,7 +257,7 @@ rule virus_specific_jsons:
     input:
         auspice_config= "config/auspice_config.json",
         pathogen = "config/pathogen.json",
-        additional_pathogen="config/pathogen.json",
+        additional_pathogen="dataset_config/{a_or_b}/{reference}/pathogen.json",
     output:
         pathogen = "build/{a_or_b}/{reference}/pathogen.json",
         auspice = "build/{a_or_b}/{reference}/auspice_config.json",

diff --git a/nextclade/dataset_config/a/EPI_ISL_412866/pathogen.json b/nextclade/dataset_config/a/EPI_ISL_412866/pathogen.json
@@ -0,0 +1,7 @@
+{
+    "shortcuts": [
+        "rsv_a",
+        "nextstrain/rsv/a",
+        "nextstrain/rsv/a/hRSV-A-England-397-2017"
+      ]
+}
diff --git a/nextclade/dataset_config/b/EPI_ISL_1653999/pathogen.json b/nextclade/dataset_config/b/EPI_ISL_1653999/pathogen.json
@@ -0,0 +1,7 @@
+{
+    "shortcuts": [
+      "rsv_b",
+      "nextstrain/rsv/b",
+      "nextstrain/rsv/b/hRSV-B-Australia-VIC-RCH056-2019"
+    ]
+}