From 1856fe85c280f3cfac443e615d2c63f04ca71f53 Mon Sep 17 00:00:00 2001
From: root <root@DOHLT-7PJFXL3.doh.wa.lcl>
Date: Fri, 14 Jul 2023 13:04:49 -0400
Subject: [PATCH] added run name to read path

---
 modules/local/prepare_generic.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/prepare_generic.nf b/modules/local/prepare_generic.nf
index 2593b3f..c623e21 100644
--- a/modules/local/prepare_generic.nf
+++ b/modules/local/prepare_generic.nf
@@ -11,7 +11,7 @@ process PREPARE_GENERIC {
 
     shell: // This script is bundled with the pipeline, in nf-core/bsfetch/bin/
     '''
-    prepare_generic.sh "!{reads}" "!{params.outdir}"
+    prepare_generic.sh "!{reads}" "!{params.outdir}/!{params.run_name}"
 
     cat <<-END_VERSIONS > versions.yml
     "!{task.process}":