From fbe8025b8e2f583767a54ace3b1dcb518d0de14f Mon Sep 17 00:00:00 2001
From: Fattigman <jacob.karlstrom@gmail.com>
Date: Thu, 29 Jun 2023 11:23:53 +0200
Subject: [PATCH] generalized web packing

---
 modules/pack_websummaries/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/pack_websummaries/main.nf b/modules/pack_websummaries/main.nf
index 19131c2..768fb1f 100644
--- a/modules/pack_websummaries/main.nf
+++ b/modules/pack_websummaries/main.nf
@@ -26,7 +26,9 @@ process PACK_WEBSUMMARIES{
         # append the file path and the sample name to the array
         file_paths+=("$file")
         dir=$(dirname "$file")
-        dir=$(dirname "$dir")
+        if ! [ $(dirname "$dir") == "per_sample_output" ]; then
+            dir=$(dirname "$dir")
+        fi
         result=$(basename "$dir")
         sample_names+=("$result")
         echo $file $result