src/dual_mapping_paired.nf : add option for better hisat splice junction

src/dual_mapping_paired.nf

@@ -96,7 +96,8 @@ 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 \
+--rna-strandness 'F' --dta --no-temp-splicesite \
+--novel-splicesite-outfile ${file_id}splicesite.txt
 2> ${file_id}_hisat2_NY5.txt | samtools view -F 4 -F 16 -Sb - > ${file_id}.bam
 """
 }
@@ -148,15 +149,24 @@ process merge_bam{
 
   input:
   set file_id, index_id, file(bam_bowtie), file(bam_hisat) from merged_bam
+  file(hisat_txt) from  hisat_report
+  file(bowtie_txt) from mapping_report
 
   output:
   file "*merged.{bam,bam.bai}" into final_flow
+  file "*.txt" into final_report
 
   """
   samtools sort -@ ${task.cpus} -o ${file_id}_bowtie_sort.bam ${bam_bowtie} && \
   samtools sort -@ ${task.cpus} -o ${file_id}_hisat_sort.bam ${bam_hisat} && \
   samtools merge ${file_id}_merged.bam *sort.bam && \
   samtools index ${file_id}_merged.bam
+
+  for i in *.txt ; do
+    echo \$i
+    cat \$i > \${i::-4}_new.txt
+  done
+
   """
 
 }