From ce83470687273003db1495506148cc8d8dd9fb16 Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Fri, 2 Oct 2020 10:09:29 +0200
Subject: [PATCH] fix beug
---
src/dual_mapping_paired.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/dual_mapping_paired.nf b/src/dual_mapping_paired.nf
index 8114230a..9852e7e4 100644
--- a/src/dual_mapping_paired.nf
+++ b/src/dual_mapping_paired.nf
@@ -98,7 +98,7 @@ process hisat2 {
"""
hisat2 -x ${index_id} -p ${task.cpus} \
-1 ${fastq_filtred[0]} -2 ${fastq_filtred[1]} --un-conc-gz ${file_id}_notaligned_hisat_R%.fastq.gz \
---rna-strandness 'F' --dta --no-temp-splicesite \
+--rna-strandness 'F' \
2> ${file_id}_hisat2_NY5.txt | samtools view -F 4 -F 16 -Sb - > ${file_id}.bam
if grep -q "ERR" ${file_id}_hisat2_NY5.txt ; then
@@ -169,7 +169,7 @@ process merge_bam{
for i in *.txt ; do
echo \$i
- cat \$i > \${i::-4}_new.txt
+ cat \$i >> \${i::-4}_new.txt
done
"""
--
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