Verified Commit 3454e1e8 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

add sge config for some modules

parent 98db0358
......@@ -12,6 +12,14 @@ profiles {
process{
$fasta_from_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
}
}
......
......@@ -15,9 +15,25 @@ profiles {
process{
$index_fasta {
beforeScript = "module purge; module load Kallisto/0.43.1"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$mapping_fastq {
beforeScript = "module purge; module load Kallisto/0.43.1"
executor = "sge"
cpus = 4
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
}
}
......
......@@ -17,7 +17,6 @@ Channel
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
......
......@@ -12,6 +12,14 @@ profiles {
process{
$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'
}
}
}
......
......@@ -12,6 +12,14 @@ profiles {
process{
$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'
}
}
}
......@@ -31,6 +39,14 @@ profiles {
process{
$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'
}
}
}
......
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