From 9a8ff6096494fd04a4556559d7829a5b80d90f53 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 31 Jul 2018 14:15:35 +0200
Subject: [PATCH] correction bowtie 2

---
 src/RNAseq_sen1D_bowtie2.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/RNAseq_sen1D_bowtie2.nf b/src/RNAseq_sen1D_bowtie2.nf
index 3b79021..3671747 100644
--- a/src/RNAseq_sen1D_bowtie2.nf
+++ b/src/RNAseq_sen1D_bowtie2.nf
@@ -214,7 +214,7 @@ process mapping_fastq {
 
   input:
   set pair_id, file(reads) from fastq_files_align
-  file index from index_files.toList()
+  file index from index_files.collect()
 
   output:
   set pair_id, "*.bam" into bam_files
@@ -228,7 +228,7 @@ process mapping_fastq {
     }
   }
 """
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
+ bowtie2 --very-sensitive --fr -p ${task.cpus} -x ${index_id} \
  -1 ${reads[0]} -2 ${reads[1]} 2> \
  ${pair_id}_bowtie2_report.txt | \
  samtools view -Sb - > ${pair_id}.bam
-- 
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