diff --git a/src/RNAseq_sen1D_bowtie2.nf b/src/RNAseq_sen1D_bowtie2.nf
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+/*
+* cutadapt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+
+/* Small RNA-seq Illumina adaptor removal NEXTflex Small RNA Seq Kit v3 */
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_R{1,2}.fastq.gz"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+fastq_files.into{fastq_files_adaptor; fastq_files_fastq}
+
+process fastqc_fastq {
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/raw", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_fastq
+
+ output:
+ file "*.{zip,html}" into fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
+${reads[0]} ${reads[1]}
+"""
+}
+
+process adaptor_removal {
+ tag "$pair_id"
+
+ input:
+ set pair_id, file(reads) from fastq_files_adaptor
+
+ output:
+ set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA \
+ -o ${pair_id}_cut_R1.fastq.gz \
+ ${reads[0]} > ${pair_id}_report.txt
+
+ cutadapt -a GATCGTCGGACTGTAGAACTCTGAAC -g GTTCAGAGTTCTACAGTCCGACGATC \
+ -o ${pair_id}_cut_R2.fastq.gz \
+ ${reads[1]} > ${pair_id}_report.txt
+ """
+}
+
+fastq_files_cut.into{fastq_files_cut_randombp; fastq_files_cut_fastq}
+
+process fastqc_fastq_cutadapt {
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/adaptor_removal/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_cut_fastq
+
+ output:
+ file "*.{zip,html}" into cutadapt_fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
+${reads[0]} ${reads[1]}
+"""
+}
+
+process random_bases_4_trimming {
+ tag "$pair_id"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_cut_randombp
+
+ output:
+ set pair_id, "*_cut4_R{1,2}.fastq.gz" into fastq_files_cut4
+
+ script:
+ """
+ cutadapt -u 4 -u -4 \
+ -o ${pair_id}_cut4_R1.fastq.gz -p ${pair_id}_cut4_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+ """
+}
+
+fastq_files_cut4.into{fastq_files_trim; fastq_files_cut4_fastq}
+
+process fastqc_fastq_randombp {
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/random_bases_4_trimming/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_cut4_fastq
+
+ output:
+ file "*.{zip,html}" into randombp_fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
+${reads[0]} ${reads[1]}
+"""
+}
+
+/*
+* urqt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/* quality trimming */
+
+/*
+* for paired-end data
+*/
+
+process trimming {
+ tag "${reads}"
+ cpus 4
+ publishDir "results/fastq/trimming/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_trim
+
+ output:
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_urqt
+
+ script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+--in ${reads[0]} --inpair ${reads[1]} \
+--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+fastq_files_urqt.into{fastq_files_align; fastq_files_urqt_fastq}
+
+process fastqc_fastq_urqt {
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/urqt/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_urqt_fastq
+
+ output:
+ file "*.{zip,html}" into urqt_fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
+${reads[0]} ${reads[1]}
+"""
+}
+
+/*
+* Bowtie2 :
+* Imputs : fastq files
+* Imputs : fasta files
+* Output : bam files
+*/
+
+/* fasta indexing */
+params.fasta = "$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" ${fasta.baseName}_bowtie2_report.txt; then
+ exit 1
+fi
+"""
+}
+
+/*
+* for paired-end data
+*/
+
+process mapping_fastq {
+ tag "$pair_id"
+ cpus 4
+ publishDir "results/mapping/bams/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_align
+ file index from index_files.toList()
+
+ output:
+ set pair_id, "*.bam" into bam_files
+ 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_id} \
+ -1 ${reads[0]} -2 ${reads[1]} 2> \
+ ${pair_id}_bowtie2_report.txt | \
+ samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+ exit 1
+fi
+"""
+}
+
+/* MultiQC */
+
+process multiqc {
+ tag "$repport"
+ publishDir "results/fastq/multiqc/", mode: 'copy'
+ cpus = 1
+
+ input:
+ file repport from fastqc_repport.collect()
+ file repport_urqt from urqt_fastqc_repport.collect()
+ file repport_cutadapt from cutadapt_fastqc_repport.collect()
+ file repport_randombp from randombp_fastqc_repport.collect()
+ output:
+ file "*multiqc_*" into multiqc_report
+
+ script:
+"""
+multiqc -f .
+"""
+}
+
+/* bams spliting */
+
+process split_bam {
+ tag "$pair_id"
+ cpus 2
+ input:
+ set pair_id, file(bam) from bam_files
+
+ output:
+ set pair_id, "*_forward.bam" into forward_bam_files
+ set pair_id, "*_reverse.bam" into reverse_bam_files
+ script:
+"""
+samtools view -hb -F 0x10 ${bam} > ${pair_id}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${pair_id}_reverse.bam
+"""
+}
+
+/* bams sorting */
+
+process sort_bam_forward {
+ tag "$pair_id"
+ cpus 4
+ publishDir "results/mapping/bams/", mode: 'copy'
+ input:
+ set pair_id, file(bam) from forward_bam_files
+
+ output:
+ set pair_id, "*_sorted.bam" into forward_sorted_bam_files
+
+ script:
+"""
+samtools sort -@ ${task.cpus} -O BAM -o ${pair_id}_forward_sorted.bam ${bam}
+"""
+}
+process sort_bam_reverse {
+ tag "$pair_id"
+ cpus 4
+ publishDir "results/mapping/bams/", mode: 'copy'
+ input:
+ set pair_id, file(bam) from reverse_bam_files
+
+ output:
+ set pair_id, "*_sorted.bam" into reverse_sorted_bam_files
+
+ script:
+"""
+samtools sort -@ ${task.cpus} -O BAM -o ${pair_id}_reverse_sorted.bam ${bam}
+"""
+}
+
+/* bams indexing */
+
+process index_bam_forward {
+ tag "$pair_id"
+ publishDir "results/mapping/bams/", mode: 'copy'
+ input:
+ set pair_id, file(bam) from forward_sorted_bam_files
+ output:
+ set pair_id, "*bam*" into forward_indexed_bam_file
+ script:
+"""
+samtools index ${bam}
+"""
+}
+
+process index_bam_reverse {
+ tag "$pair_id"
+ publishDir "results/mapping/bams/", mode: 'copy'
+ input:
+ set pair_id, file(bam) from reverse_sorted_bam_files
+ output:
+ set pair_id, "*bam*" into reverse_indexed_bam_file
+ script:
+"""
+samtools index ${bam}
+"""
+}