From 582236f7b752065430c972286f42b1e791897da1 Mon Sep 17 00:00:00 2001
From: John Huddleston <huddlej@gmail.com>
Date: Tue, 15 Oct 2024 10:44:25 -0700
Subject: [PATCH] Use full Nextclade names for all gene segments

Not all gene segments define shorter aliases (e.g., "flu_h3n2_ha"), so
we need to use the full names (e.g., "nextstrain/flu/h3n2/ha") to
download each dataset.
---
 profiles/nextclade/run-nextclade.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/profiles/nextclade/run-nextclade.smk b/profiles/nextclade/run-nextclade.smk
index e1a4445e..4adfdebb 100644
--- a/profiles/nextclade/run-nextclade.smk
+++ b/profiles/nextclade/run-nextclade.smk
@@ -13,7 +13,7 @@ rule get_nextclade_dataset_for_lineage_and_segment:
     shell:
         """
         nextclade3 dataset get \
-            -n flu_{wildcards.lineage}_{wildcards.segment} \
+            -n 'nextstrain/flu/{wildcards.lineage}/{wildcards.segment}' \
             --output-dir {output.nextclade_dir}
         """