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Unverified Commit 9fdc0424 authored by Laurent Modolo's avatar Laurent Modolo
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nf module: update executor from psmn to sge

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with 24 additions and 24 deletions
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: fasta_from_bed { withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BEDtools/2.25.0" module = "BEDtools/2.25.0"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
......
...@@ -12,7 +12,7 @@ profiles { ...@@ -12,7 +12,7 @@ profiles {
process{ process{
withname: index_fasta { withname: index_fasta {
beforeScript = "module purge; module load BWA/0.7.17" beforeScript = "module purge; module load BWA/0.7.17"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -12,7 +12,7 @@ profiles { ...@@ -12,7 +12,7 @@ profiles {
process{ process{
withname: mapping_fastq { withname: mapping_fastq {
beforeScript = "module purge; module load BWA/0.7.17" beforeScript = "module purge; module load BWA/0.7.17"
executor = "psmn" executor = "sge"
cpus = 4 cpus = 4
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -12,7 +12,7 @@ profiles { ...@@ -12,7 +12,7 @@ profiles {
process{ process{
withname: fastqc_fastq { withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5" beforeScript = "module purge; module load FastQC/0.11.5"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -12,7 +12,7 @@ profiles { ...@@ -12,7 +12,7 @@ profiles {
process{ process{
withname: fastqc_fastq { withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5" beforeScript = "module purge; module load FastQC/0.11.5"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: index_fasta { withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0" module = "Kallisto/0.44.0"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "24h" time = "24h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: mapping_fastq { withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0" module = "Kallisto/0.44.0"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "24h" time = "24h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: mapping_fastq { withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0" module = "Kallisto/0.44.0"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "24h" time = "24h"
......
...@@ -19,7 +19,7 @@ profiles { ...@@ -19,7 +19,7 @@ profiles {
withname: compute_mappability { withname: compute_mappability {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53" module = "MUSIC/6613c53"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
...@@ -28,7 +28,7 @@ profiles { ...@@ -28,7 +28,7 @@ profiles {
withname: music_preprocessing { withname: music_preprocessing {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53" module = "MUSIC/6613c53"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
...@@ -37,7 +37,7 @@ profiles { ...@@ -37,7 +37,7 @@ profiles {
withname: music_computation { withname: music_computation {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53" module = "MUSIC/6613c53"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
......
...@@ -17,7 +17,7 @@ profiles { ...@@ -17,7 +17,7 @@ profiles {
withname: fastqc_fastq { withname: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5" module = "FastQC/0.11.5"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
...@@ -28,7 +28,7 @@ profiles { ...@@ -28,7 +28,7 @@ profiles {
withname: multiqc { withname: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MultiQC/1.0" module = "MultiQC/1.0"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -16,7 +16,7 @@ profiles { ...@@ -16,7 +16,7 @@ profiles {
withname: fastqc_fastq { withname: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5" module = "FastQC/0.11.5"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
...@@ -27,7 +27,7 @@ profiles { ...@@ -27,7 +27,7 @@ profiles {
withname: multiqc { withname: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MultiQC/1.0" module = "MultiQC/1.0"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withname: mapping_fastq { withname: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7" module = "RSEM/1.3.0:SAMtools/1.7"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "24h" time = "24h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withname: mapping_fastq { withname: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7" module = "RSEM/1.3.0:SAMtools/1.7"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "30GB" memory = "30GB"
time = "24h" time = "24h"
......
...@@ -12,7 +12,7 @@ profiles { ...@@ -12,7 +12,7 @@ profiles {
process{ process{
withname: fastq_dump { withname: fastq_dump {
beforeScript = "module purge; module load SRAtoolkit/2.8.2" beforeScript = "module purge; module load SRAtoolkit/2.8.2"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "5GB" memory = "5GB"
time = "6h" time = "6h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: trimming { withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "UrQt/d62c1f8" module = "UrQt/d62c1f8"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "5GB" memory = "5GB"
time = "12h" time = "12h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: trimming { withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "UrQt/d62c1f8" module = "UrQt/d62c1f8"
executor = "psmn" executor = "sge"
cpus = 16 cpus = 16
memory = "5GB" memory = "5GB"
time = "12h" time = "12h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: adaptor_removal { withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: adaptor_removal { withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: trimming { withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
......
...@@ -13,7 +13,7 @@ profiles { ...@@ -13,7 +13,7 @@ profiles {
withName: trimming { withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14" module = "cutadapt/1.14"
executor = "psmn" executor = "sge"
cpus = 1 cpus = 1
memory = "20GB" memory = "20GB"
time = "12h" time = "12h"
......
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