add ribowave module

src/docker_modules/RiboWave/1.0/Dockerfile

+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

+#!/bin/sh
+docker build src/docker_modules/RiboWave/1.0 -t 'ribowave:1.0'

src/nf_modules/Ribowave/ribowave.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $create_annot {
+        container = "ribowave:1.0"
+      }
+      $determination_P_site {
+        container = "ribowave:1.0"
+      }
+    }
+  }
+  sge {
+    process{
+      $create_annot {
+        beforeScript = ""
+        executor = ""
+        cpus = 1
+        memory = ""
+        time = ""
+        queueSize = 1000
+        pollInterval = ''
+        queue = ''
+        penv = ''
+      }
+    }
+  }
+}

src/nf_modules/Ribowave/ribowave.nf

+/*
+* 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 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 ${params.jobname} -s /Ribowave/scripts
+"""
+}
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+params.index = "$baseDir/data/index/*.index*"
+params.mean = 200
+params.sd = 100
+
+log.info "fastq files : ${params.fastq}"
+log.info "index files : ${params.index}"
+log.info "mean read size: ${params.mean}"
+log.info "sd read size: ${params.sd}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process mapping_fastq {
+  tag "$reads.baseName"
+  cpus 4
+  publishDir "results/mapping/quantification/", mode: 'copy'
+
+  input:
+  file reads from fastq_files
+  file index from index_files.toList()
+
+  output:
+  file "*" into count_files
+
+  script:
+"""
+mkdir ${reads.baseName}
+kallisto quant -i ${index} -t ${task.cpus} --single
+--bias --bootstrap-samples 100 -o ${reads.baseName} \
+-l ${params.mean} -s ${params.sd} -o ./ \
+${reads} > ${reads.baseName}_kallisto_report.txt
+"""
+}
+

src/nf_modules/Ribowave/ribowave_command.sh

+../../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

+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 p_site {
+  publishDir "results/ribowave/P-site", 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
+"""
+}

src/nf_modules/Ribowave/test/Pipeline.nf

+/*
+* 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

+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

+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
+"""
+}