diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
new file mode 100644
index 0000000000000000000000000000000000000000..d1200ed496c77756cde525835f581b71b2528990
--- /dev/null
+++ b/src/fasta_sampler.nf
@@ -0,0 +1,18 @@
+Channel
+ .fromPath( "data/tiny_dataset/fasta/*.fasta" )
+ .set { fasta_file }
+
+process sample_fasta {
+ publishDir "results/sampling/", mode: 'copy'
+
+ input:
+file fasta from fasta_file
+
+ output:
+file "*_sample.fasta" into fasta_sample
+
+ script:
+"""
+head ${fasta} > ${fasta.baseName}_sample.fasta
+"""
+}
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
new file mode 100644
index 0000000000000000000000000000000000000000..3e8ba47bdb12f98c134ca4ebf96a2593d6ba6c2c
--- /dev/null
+++ b/src/solution_RNASeq.config
@@ -0,0 +1,172 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ cpus = 1
+ }
+ withName: trimming {
+ cpus = 4
+ container = "lbmc/urqt:d62c1f8"
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ cpus = 1
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ cpus = 1
+ }
+ withName: trimming {
+ cpus = 4
+ container = "lbmc/urqt:d62c1f8"
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ cpus = 1
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: adaptor_removal {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/cutadapt_2.1"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
+ }
+ withName: trimming {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+ penv = 'openmp32'
+
+ }
+ withName: fasta_from_bed {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bedtools_2.25.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
+ }
+ withName: index_fasta {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+ penv = 'openmp32'
+ }
+ withName: mapping_fastq {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+ penv = 'openmp32'
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: trimming {
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+}
diff --git a/src/solution_RNASeq.nf b/src/solution_RNASeq.nf
new file mode 100644
index 0000000000000000000000000000000000000000..73940d6595aa3828629292cff067fcf20d3603f0
--- /dev/null
+++ b/src/solution_RNASeq.nf
@@ -0,0 +1,111 @@
+log.info "fastq files : ${params.fastq}"
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_files }
+Channel
+ .fromPath( params.bed )
+ .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+ .set { bed_files }
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$pair_id"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+
+ cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+ """
+}
+
+process trimming {
+ tag "${reads}"
+ publishDir "results/fastq/trimming/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_cut
+
+ output:
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+
+ 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 \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+process fasta_from_bed {
+ tag "${bed.baseName}"
+ publishDir "results/fasta/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files
+ file bed from bed_files
+
+ output:
+ file "*_extracted.fasta" into fasta_files_extracted
+
+ script:
+"""
+bedtools getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
+
+process index_fasta {
+ tag "$fasta.baseName"
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files_extracted
+
+ output:
+ file "*.index*" into index_files
+ file "*_kallisto_report.txt" into index_files_report
+
+ script:
+"""
+kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
+2> ${fasta.baseName}_kallisto_report.txt
+"""
+}
+
+process mapping_fastq {
+ tag "$reads"
+ publishDir "results/mapping/quantification/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_trim
+ file index from index_files.collect()
+
+ output:
+ file "*" into counts_files
+
+ script:
+"""
+mkdir ${pair_id}
+
+kallisto quant -i ${index} -t ${task.cpus} \
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
+"""
+}