From 3454e1e89982d386018c1bf8e80d4692061522b4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 11:32:36 +0200
Subject: [PATCH] add sge config for some modules
---
src/nf_modules/BEDtools/bedtools.config | 8 ++++++++
src/nf_modules/Kallisto/kallisto.config | 16 ++++++++++++++++
src/nf_modules/Kallisto/kallisto.nf | 1 -
src/nf_modules/UrQt/urqt.config | 8 ++++++++
src/nf_modules/cutadapt/cutadapt.config | 16 ++++++++++++++++
5 files changed, 48 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/BEDtools/bedtools.config b/src/nf_modules/BEDtools/bedtools.config
index b54cadf..7230def 100644
--- a/src/nf_modules/BEDtools/bedtools.config
+++ b/src/nf_modules/BEDtools/bedtools.config
@@ -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'
}
}
}
diff --git a/src/nf_modules/Kallisto/kallisto.config b/src/nf_modules/Kallisto/kallisto.config
index 8033648..1a92bb1 100644
--- a/src/nf_modules/Kallisto/kallisto.config
+++ b/src/nf_modules/Kallisto/kallisto.config
@@ -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'
}
$mapping_fastq {
beforeScript = "module purge; module load Kallisto/0.43.1"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
}
}
}
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
index b158eee..1f21a1f 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -17,7 +17,6 @@ Channel
process index_fasta {
tag "$fasta.baseName"
- cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
diff --git a/src/nf_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
index 8e7e40e..46a8672 100644
--- a/src/nf_modules/UrQt/urqt.config
+++ b/src/nf_modules/UrQt/urqt.config
@@ -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'
}
}
}
diff --git a/src/nf_modules/cutadapt/cutadapt.config b/src/nf_modules/cutadapt/cutadapt.config
index 969ee02..07efa9b 100644
--- a/src/nf_modules/cutadapt/cutadapt.config
+++ b/src/nf_modules/cutadapt/cutadapt.config
@@ -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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