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Verified Commit 03b4c8d0 authored by Laurent Modolo's avatar Laurent Modolo
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rm Ribowave module for when it's ready

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src/docker_modules/RiboWave/1.0/Dockerfile deleted 100644 → 0
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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
src/docker_modules/RiboWave/1.0/docker_init.sh deleted 100755 → 0
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#!/bin/sh
docker build src/docker_modules/RiboWave/1.0 -t 'ribowave:1.0'
src/nf_modules/Ribowave/pipeline_PSMN.nf deleted 100644 → 0
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/*
* 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
"""
}
src/nf_modules/Ribowave/pipeline_docker.nf deleted 100644 → 0
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/*
* 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
"""
}
src/nf_modules/Ribowave/ribowave.config deleted 100644 → 0
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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'
}
}
}
}
src/nf_modules/Ribowave/ribowave.nf deleted 100644 → 0
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/*
* 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
"""
}
src/nf_modules/Ribowave/ribowave_command.sh deleted 100644 → 0
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../../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
src/nf_modules/Ribowave/test/P-site.nf deleted 100644 → 0
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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
"""
}
src/nf_modules/Ribowave/test/Pipeline.nf deleted 100644 → 0
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/*
* 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
"""
}
src/nf_modules/Ribowave/test/create_annot.nf deleted 100644 → 0
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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
"""
}
src/nf_modules/Ribowave/test/track_P_site.nf deleted 100644 → 0
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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
"""
}
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