Skip to content
Snippets Groups Projects
Commit bd4f17a9 authored by vvanoost's avatar vvanoost
Browse files

config for pipeline SE

parent e1ef7769
No related branches found
No related tags found
No related merge requests found
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"
}
$index_fasta {
container = "bowtie2:2.3.4.1"
}
$mapping_fastq {
container = "bowtie2:2.3.4.1"
}
$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'
}
$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"
}
$sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
$index_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
}
}
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment