diff --git a/src/10_ribowave.nf b/src/10_ribowave.nf
deleted file mode 100644
index a9c41c33314c05275354d84f1cc6475614a7e04b..0000000000000000000000000000000000000000
--- a/src/10_ribowave.nf
+++ /dev/null
@@ -1,121 +0,0 @@
-/*
-* Ribowave :
-* Inputs : gtf genome files
-* Inputs : bam file
-* Inputs : genome size file
-*/
-
-/* PARAMETERS */
-
-params.gtf = ""
-params.genome = ""
-params.bam = ""
-params.genomesize = ""
-
-log.info "gtf file : ${params.gtf}"
-log.info "genome fasta file : ${params.genome}"
-log.info "bam file(s) : ${params.bam}"
-log.info "genomesize file : ${params.genomesize}"
-
-Channel
- .fromPath( params.gtf )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.gtf}" }
- .set { gtf_file }
-Channel
- .fromPath( params.genome )
- .ifEmpty { error "Cannot find any fasta files matching: ${params.genome}" }
- .set { genome_file }
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .set { bam_files }
-bam_files.into {bam_deter_P_site ; bam_track_P_site}
-Channel
- .fromPath( params.genomesize )
- .ifEmpty { error "Cannot find any index files matching: ${params.genomesize}" }
- .set { genomesize_file }
-
-
-/* CREATE ANNOTATION */
-
-process create_annot {
- publishDir "results/ribowave/annotation", mode: 'copy'
-
- input:
- file gtf from gtf_file
- file genome from genome_file
-
- output:
- file "*" into annot_file
- file "start_codon.bed" into start_codon_channel
- file "final.ORFs" into finalORF_channel
- file "exons.gtf" into exon_gtf_channel
-
- script:
-"""
-/Ribowave/scripts/create_annotation.sh -G ${gtf} -f ${genome} -o ./ -s /Ribowave/scripts
-"""
-}
-
-
-/* P-site determination */
-
-process determination_P_site {
- tag "$bam.baseName"
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file bam from bam_deter_P_site
- file start from start_codon_channel
-
- output:
- file "*" into p_site_channel
- file "*psite1nt.txt" into psite1nt_channel
-
- script:
-"""
-/Ribowave/scripts/P-site_determination.sh -i ${bam} -S ${start} -o ./ -n ${bam.baseName} -s /Ribowave/scripts
-"""
-}
-
-/* P-site track */
-
-process track_P_site {
- tag "$bam.baseName"
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file bam from bam_track_P_site
- file exon from exon_gtf_channel
- file genomesize from genomesize_file
- file p_site from psite1nt_channel
-
- output:
- file "*" into track_p_site_channel
- file "final.psite" into psite_channel
-
-
- script:
-"""
-/Ribowave/scripts/create_track_Ribo.sh -i ${bam} -G ${exon} -g ${genomesize} -P ${p_site} -o ./ -n ${bam.baseName} -s /Ribowave/scripts
-"""
-}
-
-/* ribowave Identifying translated ORF */
-
-process ribowave_transORF {
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file psite from psite_channel
- file finalORF from finalORF_channel
-
- output:
- file "*" into ribowave_channel
-
- script:
-"""
-/Ribowave/scripts/Ribowave -PD -a ${psite} -b ${finalORF} -o ./ -n ${bam.baseName} -s /Ribowave/scripts -p 2
-"""
-}
-
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
deleted file mode 100644
index 3d7ab45e8d8507c2ddbc53ad2891160b1073531f..0000000000000000000000000000000000000000
--- a/src/RNAseq.nf
+++ /dev/null
@@ -1,117 +0,0 @@
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq" /* we can use now a param -fastq to specify where are fastq files. this path is the default path */
-params.fasta = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fastq files : ${params.fastq}"
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-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: ${params.bed}" }
- .set { bed_files }
-
-process adaptor_removal {
- tag "$pair_id"
- publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*_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}"
- cpus 4
- publishDir "results/fastq/trimming/", mode: 'copy'
-
- input:
- file reads from fastq_files_cut
-
- output:
- file "*_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 ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
-> ${reads[0].baseName}_trimming_report.txt
-"""
-}
-
-process fasta_from_bed {
- tag "${bed.baseName}"
- cpus 4
- 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
-
- script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
-process mapping_fastq {
- tag "$reads"
- cpus 4
- publishDir "results/mapping/quantification/", mode: 'copy'
-
- input:
- file reads from fastq_files_trim
- file index from index_files.toList()
-
- output:
- file "*" into counts_files
-
- script:
-"""
-mkdir ${reads[0].baseName}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
-"""
-}
-
-
diff --git a/src/cutadapt.config b/src/cutadapt.config
deleted file mode 100644
index 7bb81606793301c8ddde9dd4e0b143c8db51fd40..0000000000000000000000000000000000000000
--- a/src/cutadapt.config
+++ /dev/null
@@ -1,120 +0,0 @@
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $adaptor_removal {
- container = "cutadapt:1.14"
- }
- }
- }
- sge {
- process{
- $adaptor_removal {
- beforeScript = "module purge; module load cutadapt/1.14"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $trimming {
- container = "urqt:d62c1f8"
- }
- }
- }
- sge {
- process{
- $trimming {
- beforeScript = "module purge; module load UrQt/d62c1f8"
- executor = "sge"
- cpus = 4
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $fasta_from_bed {
- container = "bedtools:2.25.0"
- }
- }
- }
- sge {
- process{
- $fasta_from_bed {
- beforeScript = "module purge; module load BEDtools/2.25.0"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
-
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $index_fasta {
- container = "kallisto:0.43.1"
- }
- $mapping_fastq {
- container = "kallisto:0.43.1"
- }
- }
- }
- sge {
- process{
- $index_fasta {
- beforeScript = "module purge; module load Kallisto/0.43.1"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- $mapping_fastq {
- beforeScript = "module purge; module load Kallisto/0.43.1"
- executor = "sge"
- cpus = 4
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
deleted file mode 100644
index d1200ed496c77756cde525835f581b71b2528990..0000000000000000000000000000000000000000
--- a/src/fasta_sampler.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-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/ribowave.config b/src/ribowave.config
deleted file mode 100644
index 59e6a55d6dee082b8b54f6b2cc98391d65350087..0000000000000000000000000000000000000000
--- a/src/ribowave.config
+++ /dev/null
@@ -1,60 +0,0 @@
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $create_annot {
- container = "ribowave:1.0"
- }
- $determination_P_site {
- container = "ribowave:1.0"
- }
- $track_P_site {
- container = "ribowave:1.0"
- }
- $ribowave_transORF {
- container = "ribowave:1.0"
- }
- }
- }
- sge {
- process{
- $create_annot {
- beforeScript = "source /home/elabaron/.bashrc; module load BEDtools/2.25.0"
- executor = "sge"
- cpus = 8
- memory = "5GB"
- time = "6h"
- queue = '*-E5-2667*'
- penv = 'openmp8'
- }
- $determination_P_site {
- beforeScript = "source /home/elabaron/.bashrc; module load BEDtools/2.25.0"
- executor = "sge"
- cpus = 8
- memory = "5GB"
- time = "6h"
- queue = '*-E5-2667*'
- penv = 'openmp8'
- }
- $track_P_site {
- beforeScript = "source /home/elabaron/.bashrc; module load BEDtools/2.25.0"
- executor = "sge"
- cpus = 8
- memory = "5GB"
- time = "6h"
- queue = '*-E5-2667*'
- penv = 'openmp8'
- }
- $ribowave_transORF {
- beforeScript = "source /home/elabaron/.bashrc; module load BEDtools/2.25.0"
- executor = "sge"
- cpus = 8
- memory = "128GB"
- time = "6h"
- queue = '*-E5-2667*'
- penv = 'openmp8'
- }
- }
- }
-}