From 03b4c8d032c0f1288fb7046533092e99f13c1b24 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 25 Jul 2018 13:54:48 +0200
Subject: [PATCH] rm Ribowave module for when it's ready

---
 src/docker_modules/RiboWave/1.0/Dockerfile    |  18 --
 .../RiboWave/1.0/docker_init.sh               |   2 -
 src/nf_modules/Ribowave/pipeline_PSMN.nf      | 121 -------------
 src/nf_modules/Ribowave/pipeline_docker.nf    | 121 -------------
 src/nf_modules/Ribowave/ribowave.config       |  60 -------
 src/nf_modules/Ribowave/ribowave.nf           | 167 ------------------
 src/nf_modules/Ribowave/ribowave_command.sh   |   1 -
 src/nf_modules/Ribowave/test/P-site.nf        |  32 ----
 src/nf_modules/Ribowave/test/Pipeline.nf      |  63 -------
 src/nf_modules/Ribowave/test/create_annot.nf  |  31 ----
 src/nf_modules/Ribowave/test/track_P_site.nf  |  46 -----
 11 files changed, 662 deletions(-)
 delete mode 100644 src/docker_modules/RiboWave/1.0/Dockerfile
 delete mode 100755 src/docker_modules/RiboWave/1.0/docker_init.sh
 delete mode 100644 src/nf_modules/Ribowave/pipeline_PSMN.nf
 delete mode 100644 src/nf_modules/Ribowave/pipeline_docker.nf
 delete mode 100644 src/nf_modules/Ribowave/ribowave.config
 delete mode 100644 src/nf_modules/Ribowave/ribowave.nf
 delete mode 100644 src/nf_modules/Ribowave/ribowave_command.sh
 delete mode 100644 src/nf_modules/Ribowave/test/P-site.nf
 delete mode 100644 src/nf_modules/Ribowave/test/Pipeline.nf
 delete mode 100644 src/nf_modules/Ribowave/test/create_annot.nf
 delete mode 100644 src/nf_modules/Ribowave/test/track_P_site.nf

diff --git a/src/docker_modules/RiboWave/1.0/Dockerfile b/src/docker_modules/RiboWave/1.0/Dockerfile
deleted file mode 100644
index 2d7b5112..00000000
--- 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 871171a5..00000000
--- 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 9819ff18..00000000
--- 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 9c9ff82a..00000000
--- 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 8401a596..00000000
--- 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 b611648e..00000000
--- 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 2b401e9d..00000000
--- 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 e1211223..00000000
--- 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 894dc48d..00000000
--- 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 058d9117..00000000
--- 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 d36ab485..00000000
--- 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
-"""
-}
-- 
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