RNAseq_sen1D.nf: fix bowtie2 index problem

src/RNAseq_sen1D.nf

@@ -221,8 +221,14 @@ process mapping_fastq {
   file "*_bowtie2_report.txt" into mapping_fastq_report
 
   script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/) ) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
 """
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
+ bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
  -1 ${reads[0]} -2 ${reads[1]} 2> \
  ${pair_id}_bowtie2_report.txt | \
  samtools view -Sb - > ${pair_id}.bam