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Commit b005ff34 authored by elabaron's avatar elabaron
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add process in ribowave

parent 3884efc1
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......@@ -9,20 +9,59 @@ profiles {
$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 = ""
executor = ""
beforeScript = "module purge; module load BEDtools/2.25.0; module load R/3.4.3"
executor = "sge"
cpus = 1
memory = "10Go"
time = "1h"
queueSize = 1000
pollInterval = ''
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$determination_P_site {
beforeScript = "module purge; module load BEDtools/2.25.0; module load R/3.4.3"
executor = "sge"
cpus = 1
memory = "10Go"
time = "1h"
queueSize = 1000
pollInterval = ''
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$track_P_site {
beforeScript = "module purge; module load BEDtools/2.25.0; module load R/3.4.3"
executor = "sge"
cpus = 1
memory = ""
time = ""
memory = "10Go"
time = "1h"
queueSize = 1000
pollInterval = ''
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$ribowave_transORF {
beforeScript = "module purge; module load BEDtools/2.25.0; module load R/3.4.3"
executor = "sge"
cpus = 8
memory = "10Go"
time = "6h"
queueSize = 1000
pollInterval = ''
queue = ''
penv = ''
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
}
}
......
......@@ -108,8 +108,8 @@ Channel
.ifEmpty { error "Cannot find any index files matching: ${params.p_site}" }
.set { p_site_file }
process determination_P_site {
publishDir "results/ribowave/track_P_site", mode: 'copy'
process track_P_site {
publishDir "results/ribowave", mode: 'copy'
input:
file bam from bam_files
......@@ -118,7 +118,7 @@ process determination_P_site {
file p_site from p_site_file
output:
file "*" into det_p_site_channel
file "*" into track_p_site_channel
script:
"""
......@@ -127,47 +127,41 @@ process determination_P_site {
}
/*
* for single-end data
* ribowave Identifying translated ORF
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
params.mean = 200
params.sd = 100
params.psite = ""
params.finalORF = ""
params.outputdir = ""
params.jobname = ""
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}"
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.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
.fromPath( params.psite )
.ifEmpty { error "Cannot find any fastq files matching: ${params.psite}" }
.set { psite_file }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
.fromPath( params.finalORF )
.ifEmpty { error "Cannot find any index files matching: ${params.finalORF}" }
.set { finalORF_file }
process mapping_fastq {
tag "$reads.baseName"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
process ribowave_transORF {
publishDir "results/ribowave", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
file psite from psite_file
file finalORF from finalORF_file
output:
file "*" into count_files
file "*" into ribowave_channel
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
/Ribowave/scripts/Ribowave -PD -a ${psite} -b ${finalORF} -o ${params.outputdir} -n ${params.jobname} -s /Ribowave/scripts -p 8
"""
}
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