change cut to cut4 in trimming process

src/RNAseq_sen1D.nf

@@ -48,7 +48,7 @@ process 4_random_bases_trimming {
   set pair_id, file(reads) from fastq_files_cut
 
   output:
-  set pair_id, "*_cut4_R{1,2}.fastq.gz" into fastq_files_cut
+  set pair_id, "*_cut4_R{1,2}.fastq.gz" into fastq_files_cut4
 
   script:
   """
@@ -87,3 +87,86 @@ UrQt --t 20 --m ${task.cpus} --gz \
 > ${pair_id}_trimming_report.txt
 """
 }
+
+/*
+* Bowtie2 :
+* Imputs : fastq files
+* Imputs : fasta files
+* Output : bam files
+*/
+
+/*                      fasta indexing                                     */
+params.fasta = "$baseDir/data/bam/*.fasta"
+
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .set { fasta_file }
+
+process index_fasta {
+  tag "$fasta.baseName"
+  cpus 4
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    file fasta from fasta_file
+
+  output:
+    file "*.index*" into index_files
+
+  script:
+"""
+bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}
+
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+params.index = "$baseDir/data/index/*.index.*"
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$pair_id"
+  cpus 4
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+  file index from index_files.toList()
+
+  output:
+  set pair_id, "*.bam" into bam_files
+
+  script:
+"""
+ bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
+ -1 ${reads[0]} -2 ${reads[1]} 2> \
+ ${pair_id}_bowtie2_report.txt | \
+ samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+  exit 1
+fi
+"""
+}