From 490ff2846124ed28cc93c346f8b31b66e20c277d Mon Sep 17 00:00:00 2001
From: james hadfield <hadfield.james@gmail.com>
Date: Fri, 26 Apr 2024 10:11:57 +1200
Subject: [PATCH] Inline root sequence

The sequence size is small relative to the typical dataset size and for
a full run reduces the number of output auspice files from 96 to 48.
---
 Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 70c172d..1883378 100755
--- a/Snakefile
+++ b/Snakefile
@@ -430,7 +430,7 @@ rule export:
             --lat-longs {input.lat_longs} \
             --auspice-config {input.auspice_config} \
             --description {input.description} \
-            --include-root-sequence \
+            --include-root-sequence-inline \
             --output {output.auspice_json}
         """