diff --git a/entrypoint-aws-batch b/entrypoint-aws-batch
index ae92419..a56371c 100755
--- a/entrypoint-aws-batch
+++ b/entrypoint-aws-batch
@@ -40,8 +40,8 @@ case "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" in
                 return "$zipstatus"
             fi
         }
-        zip -u "$PWD.zip" -r . --exclude ".snakemake/*"     || succeed-when-nothing-to-update $?
-        zip -u "$PWD.zip" -r . --include ".snakemake/log/*" || succeed-when-nothing-to-update $?
+        zip -u "$PWD.zip" -r . --exclude ".snakemake/*"                             || succeed-when-nothing-to-update $?
+        zip -u "$PWD.zip" -r . --include ".snakemake/log/*" ".snakemake/metadata/*" || succeed-when-nothing-to-update $?
         aws s3 cp --no-progress "$PWD.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"
         ;;
     s3://*)