From 7ef2a978829274606974750e0d53578ceacd83e4 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:28:41 +0200
Subject: [PATCH] Update tools/hisat2/main.nf

---
 tools/hisat2/main.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/hisat2/main.nf b/tools/hisat2/main.nf
index e9d33993..55e6fe78 100644
--- a/tools/hisat2/main.nf
+++ b/tools/hisat2/main.nf
@@ -52,9 +52,7 @@ process HISAT2 {
         hisat_name = name + "_" + params.genome["name"]
 
         """
-        module load hisat2
-        module load samtools
         hisat2 -p ${cores} ${hisat_options} -x ${index} ${splices} ${readString}  2>${hisat_name}_hisat2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${hisat_name}_hisat2.bam
         """
 
-}
\ No newline at end of file
+}