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Commit ed67f90c authored by vvanoost's avatar vvanoost
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add fastqc and multiqc to config

parent 18ea02b0
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profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqc_fastq {
container = "fastqc:0.11.5"
}
}
}
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'
}
}
}
}
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqc_fastq_cutadapt {
container = "fastqc:0.11.5"
}
}
}
sge {
process{
$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'
}
}
}
}
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqc_fastq_randombp {
container = "fastqc:0.11.5"
}
}
}
sge {
process{
$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'
}
}
}
}
profiles { profiles {
docker { docker {
docker.temp = 'auto' docker.temp = 'auto'
...@@ -131,3 +209,41 @@ profiles { ...@@ -131,3 +209,41 @@ profiles {
} }
} }
} }
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqc_fastq {
container = "fastqc:0.11.5"
}
$multiqc {
container = "multiqc:1.0"
}
}
}
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'
}
$multiqc {
beforeScript = "module purge; module load FastQC/1.0"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
}
}
}
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