diff --git a/src/docker_modules/RiboWave/1.0/Dockerfile b/src/docker_modules/RiboWave/1.0/Dockerfile
deleted file mode 100644
index 2d7b51127159576c5da53a9705e85b4862751eb5..0000000000000000000000000000000000000000
--- a/src/docker_modules/RiboWave/1.0/Dockerfile
+++ /dev/null
@@ -1,18 +0,0 @@
-FROM ubuntu:16.04
-MAINTAINER Emmanuel Labaronne
-
-ENV BEDTOOLS_VERSION=2.25.0*
-ENV PACKAGES bedtools=${BEDTOOLS_VERSION}* \
- r-base \
- r-base-dev \
- git
-
-RUN apt-get update &&\
- apt-get install -y --no-install-recommends ${PACKAGES} && \
- apt-get clean
-
-RUN printf "install.packages(c('reshape','ggplot2','wmtsa','parallel'), dep=TRUE, repos='http://cran.us.r-project.org') \n source('http://bioconductor.org/biocLite.R') \n biocLite('rhdf5')" > installpackages.R && \
-Rscript installpackages.R
-
-RUN git clone https://github.com/lulab/Ribowave.git &&\
- chmod -R +x Ribowave/scripts
diff --git a/src/docker_modules/RiboWave/1.0/docker_init.sh b/src/docker_modules/RiboWave/1.0/docker_init.sh
deleted file mode 100755
index 871171a5bcae24c7aab7be2dece93ef741cc3301..0000000000000000000000000000000000000000
--- a/src/docker_modules/RiboWave/1.0/docker_init.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-docker build src/docker_modules/RiboWave/1.0 -t 'ribowave:1.0'
diff --git a/src/nf_modules/Ribowave/pipeline_PSMN.nf b/src/nf_modules/Ribowave/pipeline_PSMN.nf
deleted file mode 100644
index 9819ff187c3e10ad937f7c54343ba3d200c071e3..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/pipeline_PSMN.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 ; bam_ribowave}
-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 "exons.gtf" into exon_gtf_channel
- file "final.ORFs" into finalORF_channel
-
- script:
-"""
-/Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts/create_annotation.sh -G ${gtf} -f ${genome} -o ./ -s /Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts
-"""
-}
-
-
-/* P-site determination */
-
-process determination_P_site {
- tag "$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 "P-site/*1nt.txt" into psite1nt_channel
-
- script:
-"""
-/Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts/P-site_determination.sh -i ${bam} -S ${start} -o ./ -n ${bam.baseName} -s /Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts
-"""
-}
-
-/* P-site track */
-process track_P_site {
- tag "$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 "bedgraph/${bam.baseName}/final.psite" into psite_channel
-
-
- script:
-"""
-/Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts/create_track_Ribo.sh -i ${bam} -G ${exon} -g ${genomesize} -P ${p_site} -o ./ -n ${bam.baseName} -s /Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts
-"""
-}
-/* ribowave Identifying translated ORF */
-
-process ribowave_transORF {
- tag "$bam.baseName"
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file psite from psite_channel
- file bam from bam_ribowave
- file finalORF from finalORF_channel
-
- output:
- file "*" into ribowave_channel
-
- script:
-"""
-/Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts/Ribowave -PD -a ${psite} -b ${finalORF} -o ./ -n ${bam.baseName} -s /Xnfs/lbmcdb/Ricci_team/shared_data/softwares/Ribowave/scripts -p 16
-"""
-}
-
diff --git a/src/nf_modules/Ribowave/pipeline_docker.nf b/src/nf_modules/Ribowave/pipeline_docker.nf
deleted file mode 100644
index 9c9ff82aac8ce1ffc356c678cc1cc91a3adcc745..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/pipeline_docker.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 ; bam_ribowave}
-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 "exons.gtf" into exon_gtf_channel
- file "final.ORFs" into finalORF_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 "P-site/*1nt.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 "bedgraph/${bam.baseName}/final.psite" into psite_channel
-
-
- script:
-"""
-/Ribowave/scripts/create_track_Ribo.sh -i ${bam} -G ${exon} -g ${genomesize} -P ${p_site} -o ./ -n ${bam.baseName} -s /Ribowave/scripts
-"""
-}
-/* ribowave Identifying translated ORF */
-
-process ribowave_transORF {
- tag "$bam.baseName"
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file psite from psite_channel
- file bam from bam_ribowave
- 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/nf_modules/Ribowave/ribowave.config b/src/nf_modules/Ribowave/ribowave.config
deleted file mode 100644
index 8401a596454ad893d7392eedbfcf3db91bbf54af..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/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 = 16
- memory = "128GB"
- time = "6h"
- queue = '*E5-2667*'
- penv = 'openmp16'
- }
- }
- }
-}
diff --git a/src/nf_modules/Ribowave/ribowave.nf b/src/nf_modules/Ribowave/ribowave.nf
deleted file mode 100644
index b611648e6b737363a09618490a62543b64bc70b5..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/ribowave.nf
+++ /dev/null
@@ -1,167 +0,0 @@
-/*
-* Ribowave :
-* Inputs : fastq files
-* Inputs : fasta files
-* Output : bam files
-*/
-
-/* Create annotation */
-params.gtf = "/media/manu/ManuDisque/gencode/gencode.v28.annotation.gtf"
-params.genome = "/media/manu/ManuDisque/gencode/GRCh38.p12.genome.fa"
-
-log.info "gtf file : ${params.gtf}"
-log.info "genome fasta file : ${params.genome}"
-
-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 }
-
-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
-
- script:
-"""
-/Ribowave/scripts/create_annotation.sh -G ${gtf} -f ${genome} -o ./ -s /Ribowave/scripts
-"""
-}
-
-
-/*
-* P-site determination
-*/
-
-params.bam = ""
-params.start = ""
-params.jobname = ""
-
-log.info "bam file(s) : ${params.bam}"
-log.info "start_codon file : ${params.start}"
-log.info "job name : ${params.jobname}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .set { bam_files }
-Channel
- .fromPath( params.start )
- .ifEmpty { error "Cannot find any index files matching: ${params.start}" }
- .set { start_file }
-
-process determination_P_site {
- publishDir "results/ribowave/", mode: 'copy'
-
- input:
- file bam from bam_files
- file start from start_file
-
- output:
- file "*" into p_site_channel
-
- script:
-"""
-/Ribowave/scripts/P-site_determination.sh -i ${bam} -S ${start} -o ./ -n ${params.jobname} -s /Ribowave/scripts
-"""
-}
-
-/*
-* P-site track
-*/
-
-params.bam = ""
-params.exon = ""
-params.genome = ""
-params.jobname = ""
-params.p_site = ""
-
-log.info "bam file(s) : ${params.bam}"
-log.info "exon file : ${params.exon}"
-log.info "genome file : ${params.genome}"
-log.info "job name : ${params.jobname}"
-log.info "job name : ${params.p_site}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .set { bam_files }
-Channel
- .fromPath( params.exon )
- .ifEmpty { error "Cannot find any index files matching: ${params.exon}" }
- .set { exon_file }
-Channel
- .fromPath( params.genome )
- .ifEmpty { error "Cannot find any index files matching: ${params.genome}" }
- .set { genome_file }
-Channel
- .fromPath( params.p_site )
- .ifEmpty { error "Cannot find any index files matching: ${params.p_site}" }
- .set { p_site_file }
-
-process track_P_site {
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file bam from bam_files
- file exon from exon_file
- file genome from genome_file
- file p_site from p_site_file
-
- output:
- file "*" into track_p_site_channel
-
- script:
-"""
-/Ribowave/scripts/create_track_Ribo.sh -i ${bam} -G ${exon} -g ${genome} -P ${p_site} -o ./ -n ${params.jobname} -s /Ribowave/scripts
-"""
-}
-
-/*
-* ribowave Identifying translated ORF
-*/
-
-params.psite = ""
-params.finalORF = ""
-params.outputdir = ""
-params.jobname = ""
-
-log.info "psite file : ${params.psite}"
-log.info "finalORF file : ${params.finalORF}"
-log.info "job name : ${params.jobname}"
-log.info "output dir : ${params.outputdir}"
-
-Channel
- .fromPath( params.psite )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.psite}" }
- .set { psite_file }
-Channel
- .fromPath( params.finalORF )
- .ifEmpty { error "Cannot find any index files matching: ${params.finalORF}" }
- .set { finalORF_file }
-
-process ribowave_transORF {
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file psite from psite_file
- file finalORF from finalORF_file
-
- output:
- file "*" into ribowave_channel
-
- script:
-"""
-/Ribowave/scripts/Ribowave -PD -a ${psite} -b ${finalORF} -o ${params.outputdir} -n ${params.jobname} -s /Ribowave/scripts -p 8
-"""
-}
-
diff --git a/src/nf_modules/Ribowave/ribowave_command.sh b/src/nf_modules/Ribowave/ribowave_command.sh
deleted file mode 100644
index 2b401e9dba2ff9b99e5fb3e21689ca0181a6704c..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/ribowave_command.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../nextflow/nextflow src/nf_modules/Ribowave/test/Pipeline.nf -resume -with-dag results/ribowave_dag.pdf -with-timeline results/ribowave_timeline -c src/nf_modules/Ribowave/ribowave.config -profile docker --gtf /media/manu/ManuDisque/gencode/gencode.v27.annotation.gtf --genome /media/manu/ManuDisque/gencode/GRCh38.p10.genome.fa --bam /media/manu/ManuDisque/HIV_project/hg38/U937_CHX_hg38_allmerge_uniqMapped_sorted.bam --jobname U937_CHY_merged
diff --git a/src/nf_modules/Ribowave/test/P-site.nf b/src/nf_modules/Ribowave/test/P-site.nf
deleted file mode 100644
index e12112236ed74b897b2bfafe70b3b2d593d35b7b..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/test/P-site.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-params.bam = ""
-params.start = ""
-
-log.info "bam file(s) : ${params.bam}"
-log.info "start_codon file : ${params.start}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .set { bam_files }
-Channel
- .fromPath( params.start )
- .ifEmpty { error "Cannot find any index files matching: ${params.start}" }
- .set { start_file }
-
-process determination_P_site {
- tag "$bam.baseName"
- publishDir "results/ribowave", mode: 'copy'
-
- input:
- file bam from bam_files
- file start from start_file
-
- 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
-"""
-}
diff --git a/src/nf_modules/Ribowave/test/Pipeline.nf b/src/nf_modules/Ribowave/test/Pipeline.nf
deleted file mode 100644
index 894dc48da6167d20931872a71becbe6015170cb5..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/test/Pipeline.nf
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
-* Ribowave :
-* Inputs : fastq files
-* Inputs : fasta files
-* Output : bam files
-*/
-
-params.gtf = "/media/manu/ManuDisque/gencode/gencode.v28.annotation.gtf"
-params.genome = "/media/manu/ManuDisque/gencode/GRCh38.p12.genome.fa"
-params.bam = ""
-params.jobname = ""
-
-log.info "gtf file : ${params.gtf}"
-log.info "genome fasta file : ${params.genome}"
-log.info "bam file(s) : ${params.bam}"
-log.info "job name : ${params.jobname}"
-
-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 }
-
-process create_annot {
- publishDir "results/ribowave/gtf27/annot", mode: 'copy'
-
- input:
- file gtf from gtf_file
- file genome from genome_file
-
- output:
- file "*" into annot_file_save
- file "start_codon.bed" into annot_file
-
- script:
-"""
-/Ribowave/scripts/create_annotation.sh -G ${gtf} -f ${genome} -o ./ -s /Ribowave/scripts
-"""
-}
-
-process determination_P_site {
- publishDir "results/ribowave/gtf27/deter_P_site", mode: 'copy'
-
- input:
- file bam from bam_files
- file start from annot_file
-
- output:
- file "*" into p_site_channel
-
- script:
-"""
-/Ribowave/scripts/P-site_determination.sh -i ${bam} -S ${start} -o ./ -n ${params.jobname} -s /Ribowave/scripts
-"""
-}
-
diff --git a/src/nf_modules/Ribowave/test/create_annot.nf b/src/nf_modules/Ribowave/test/create_annot.nf
deleted file mode 100644
index 058d911719921afc241c63b7b2c88ec3fb72fb71..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/test/create_annot.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-params.gtf = "/media/manu/ManuDisque/gencode/gencode.v28.annotation.gtf"
-params.genome = "/media/manu/ManuDisque/gencode/GRCh38.p12.genome.fa"
-
-log.info "gtf file : ${params.gtf}"
-log.info "genome fasta file : ${params.genome}"
-
-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 }
-
-process create_annot {
- publishDir "results/ribowave/", mode: 'copy'
-
- input:
- file gtf from gtf_file
- file genome from genome_file
-
- output:
- file "*" into annot_file
-
- script:
-"""
-mkdir annotation
-/Ribowave/scripts/create_annotation.sh -G ${gtf} -f ${genome} -o annotation -s /Ribowave/scripts
-"""
-}
diff --git a/src/nf_modules/Ribowave/test/track_P_site.nf b/src/nf_modules/Ribowave/test/track_P_site.nf
deleted file mode 100644
index d36ab485d714e88662c07ae52c47962372e06079..0000000000000000000000000000000000000000
--- a/src/nf_modules/Ribowave/test/track_P_site.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-params.bam = ""
-params.exon = ""
-params.genome = ""
-params.jobname = ""
-params.p_site = ""
-
-log.info "bam file(s) : ${params.bam}"
-log.info "exon file : ${params.exon}"
-log.info "genome file : ${params.genome}"
-log.info "job name : ${params.jobname}"
-log.info "job name : ${params.p_site}"
-
-Channel
- .fromPath( params.bam )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
- .set { bam_files }
-Channel
- .fromPath( params.exon )
- .ifEmpty { error "Cannot find any index files matching: ${params.exon}" }
- .set { exon_file }
-Channel
- .fromPath( params.genome )
- .ifEmpty { error "Cannot find any index files matching: ${params.genome}" }
- .set { genome_file }
-Channel
- .fromPath( params.p_site )
- .ifEmpty { error "Cannot find any index files matching: ${params.p_site}" }
- .set { p_site_file }
-
-process determination_P_site {
- publishDir "results/ribowave/track_P_site", mode: 'copy'
-
- input:
- file bam from bam_files
- file exon from exon_file
- file genome from genome_file
- file p_site from p_site_file
-
- output:
- file "*" into det_p_site_channel
-
- script:
-"""
-/Ribowave/scripts/create_track_Ribo.sh -i ${bam} -G ${exon} -g ${genome} -P ${p_site} -o ./ -n ${params.jobname} -s /Ribowave/scripts
-"""
-}