Commit 8f51fbe1 authored by fmortreu's avatar fmortreu
Browse files

RNAseq_confg+nf

parent 98d41e6f
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
withName: adaptor_removal {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
withName: trimming {
cpus = 4
container = "lbmc/urqt:d62c1f8"
}
}
}
singularity {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
}
psmn{
process{
withName: adaptor_removal {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
}
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
}
}
}
log.info "fastq files : ${params.fastq}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process adaptor_removal {
tag "$pair_id"
publishDir "results/fastq/adaptor_removal/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
output:
set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
process trimming {
tag "${reads}"
publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
output:
set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
> ${pair_id}_trimming_report.txt
"""
}
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