From cf75becc7ede32f2b9b26050d8cfa0e6032a7dcd Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 25 Jun 2018 16:44:38 -0500
Subject: [PATCH] Fix paired end issu.e
---
workflow/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 31ab992..9cd780d 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -126,7 +126,7 @@ process alignReads {
if (pairedEnd) {
"""
- python3 $baseDir/scripts/map_reads.py -f $reads -r ${index}/genome.fa -p
+ python3 $baseDir/scripts/map_reads.py -f ${reads[0]} ${reads[1]} -r ${index}/genome.fa -p
"""
}
else {
--
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