Merge branch 'master' of gitbio.ens-lyon.fr:LBMC/RMI2/rmi2_pipelines

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
 
   """