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Commit 15bc6ba1 authored by vvanoost's avatar vvanoost
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CCA removal from mature tRNA

parent 1814df72
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profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqc_fastq {
container = "fastqc:0.11.5"
}
$fastqc_fastq_cutadapt {
container = "fastqc:0.11.5"
}
$fastqc_fastq_randombp {
container = "fastqc:0.11.5"
}
$fastqc_fastq_urqt {
container = "fastqc:0.11.5"
}
$adaptor_removal {
container = "cutadapt:1.14"
}
$multiqc {
container = "multiqc:1.0"
}
$random_bases_4_trimming {
container = "cutadapt:1.14"
}
$trimming {
container = "urqt:d62c1f8"
}
$CCA_removal {
container = "cutadapt:1.14"
}
$index_fasta {
container = "bowtie2:2.3.4.1"
}
$mapping_fastq {
container = "bowtie2:2.3.4.1"
}
$quality_filtered_bam {
container = "samtools:1.7"
}
$sort_bam {
container = "samtools:1.7"
}
$index_bam {
container = "samtools:1.7"
}
}
}
sge {
process{
$fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
$fastqc_fastq_cutadapt {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
$fastqc_fastq_randombp {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
$fastqc_fastq_urqt {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
$multiqc {
beforeScript = "module purge; module load FastQC/1.0"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
$adaptor_removal {
beforeScript = "module purge; module load cutadapt/1.14"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$random_bases_4_trimming {
beforeScript = "module purge; module load cutadapt/1.14"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$trimming {
beforeScript = "module purge; module load UrQt/d62c1f8"
executor = "sge"
cpus = 4
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$CCA_removal {
beforeScript = "module purge; module load cutadapt/1.14"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$index_fasta {
beforeScript = "module purge; module load Bowtie2/2.3.4.1"
}
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
$quality_filtered_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
$sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
$index_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
}
}
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