diff --git a/src/dual_mapping.config b/src/dual_mapping.config
new file mode 100644
index 0000000000000000000000000000000000000000..fdf3c362c7b45fb23ffe5bf44ddcdf15bbb0a964
--- /dev/null
+++ b/src/dual_mapping.config
@@ -0,0 +1,86 @@
+profiles {
+ sge {
+ process{
+ withName: index_fasta_hisat {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "hisat2/2.1.0:samtools/1.7"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ memory = "20GB"
+ cpus = 16
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: index_fasta_bowtie {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie_1.2.2"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ memory = "20GB"
+ cpus = 16
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: hisat2 {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "hisat2/2.1.0:samtools/1.7"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ memory = "20GB"
+ cpus = 16
+ time = "12h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: sort_bam {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ }
+ withName: merge_bam {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: index_fasta_hisat {
+ cpus = 4
+ container = "lbmc/hisat2:2.1.0"
+ }
+ withName: index_fasta_bowtie {
+ cpus = 4
+ container = "lbmc/bowtie:1.2.2"
+ }
+ withName: hisat2 {
+ cpus = 4
+ container = "lbmc/hisat2:2.1.0"
+ }
+ withName: bowtie {
+ cpus = 4
+ container = "lbmc/bowtie:1.2.2"
+ }
+ withName: merge_bam {
+ container = "lbmc/samtools:1.7"
+ cpus = 4
+ }
+ }
+ }
+}
diff --git a/src/dual_mapping.nf b/src/dual_mapping.nf
new file mode 100644
index 0000000000000000000000000000000000000000..c8509b9a7b698ebd6a35c0507cf042a887ab4ccc
--- /dev/null
+++ b/src/dual_mapping.nf
@@ -0,0 +1,163 @@
+///////////////////////////////////////////////////////////////////////////////
+////////////////////////////// INDEXING GENOMES /////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
+params.fasta = "data/genome/NC001802.1.fa"
+log.info "fasta files : ${params.fasta}"
+
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_file }
+
+fasta_file.into{fasta_hisat ; fasta_bowtie}
+
+/* HISAT */
+process index_fasta_hisat {
+ tag "$fasta.baseName"
+ publishDir "data/indexes/${fasta.baseName}_hisat/", mode: 'copy'
+
+ input:
+ file fasta from fasta_hisat
+
+ output:
+ file "*ht2" into index_files_hisat
+
+ script:
+"""
+hisat2-build -p ${task.cpus} ${fasta} ${fasta.baseName}
+"""
+}
+
+/* BOWTIE 1 */
+
+process index_fasta_bowtie {
+ tag "$fasta.baseName"
+ publishDir "results/${fasta.baseName}_bowtie/", mode: 'copy'
+
+ input:
+ file fasta from fasta_bowtie
+
+ output:
+ file "*ebwt" into index_files_bowtie
+ file "*_report.txt" into indexing_report
+
+ script:
+"""
+bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName} \
+&> ${fasta.baseName}_bowtie_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
+ exit 1
+fi
+"""
+}
+
+///////////////////////////////////////////////////////////////////////////////
+////////////////////////////// MAPPING GENOMES /////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+// params.index = "$baseDir/data/index/*.index*"
+
+log.info "fastq files : ${params.fastq}"
+// log.info "index files : ${params.index}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+ .set { fastq_files }
+/*Channel
+ .fromPath( params.index )
+ .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+ .set { index_files }*/
+
+/* HISAIT */
+
+process hisat2 {
+ tag "$file_id"
+
+ input:
+ set file_id, file(fastq_filtred) from fastq_files
+ file index from index_files_hisat.collect()
+
+ output:
+ set file_id, "*.bam" into bam_hisat
+ file "*.txt" into hisat_report
+ set file_id, "*.fastq.gz" into reads_non_aligned
+
+ script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
+ }
+ }
+"""
+hisat2 -x ${index_id} -p ${task.cpus} \
+-U ${fastq_filtred} --un-gz ${file_id}_notaligned_hisat.fastq.gz \
+--end-to-end --rna-strandness 'F' \
+2> ${file_id}_hisat2_NY5.txt | samtools view -F 4 -F 16 -Sb - > ${file_id}.bam
+"""
+}
+
+/* BOWTIE */
+
+process bowtie {
+ tag "$file_id"
+
+ input:
+ set file_id, file(reads) from reads_non_aligned
+ file index from index_files_bowtie.collect()
+
+ output:
+ set file_id, index_id, "*.bam" into bam_bowtie
+ file "*_report.txt" into mapping_report
+
+ script:
+index_id = index[0]
+for (index_file in index) {
+ if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
+ index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
+ }
+}
+"""
+bowtie --best --fr -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-q ${reads} 2> \
+${file_id}_bowtie_report_tmp.txt | \
+samtools view -F 4 -F 16 -Sb - > ${file_id}_bowtie.bam
+
+if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+ exit 1
+fi
+tail -n 19 ${file_id}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
+"""
+}
+
+///////////////////////////////////////////////////////////////////////////////
+////////////////////////////// MERGE BAM /////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
+bam_bowtie.join(bam_hisat)
+ .set{merged_bam}
+
+//merged_bam.println()
+
+process merge_bam{
+ publishDir "results/05_${index_id}_mergedBAM/", mode: 'copy'
+
+ input:
+ set file_id, index_id, file(bam_bowtie), file(bam_hisat) from merged_bam
+
+ output:
+ file "*merged.{bam,bam.bai}" into final_flow
+
+ """
+ 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
+ """
+
+}