correction bowtie 2

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