From 9fdc0424e39eede03f99fc8ee03c4663de08a5e9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:26:11 +0200
Subject: [PATCH] nf module: update executor from psmn to sge
---
src/nf_modules/BEDtools/fasta_from_bed.config | 2 +-
src/nf_modules/BWA/indexing.config | 2 +-
src/nf_modules/BWA/mapping_paired.config | 2 +-
src/nf_modules/FastQC/fastqc_paired.config | 2 +-
src/nf_modules/FastQC/fastqc_single.config | 2 +-
src/nf_modules/Kallisto/indexing.config | 2 +-
src/nf_modules/Kallisto/mapping_paired.config | 2 +-
src/nf_modules/Kallisto/mapping_single.config | 2 +-
src/nf_modules/MUSIC/peak_calling_single.config | 6 +++---
src/nf_modules/MultiQC/multiqc_paired.config | 4 ++--
src/nf_modules/MultiQC/multiqc_single.config | 4 ++--
src/nf_modules/RSEM/quantification_paired.config | 2 +-
src/nf_modules/RSEM/quantification_single.config | 2 +-
src/nf_modules/SRAtoolkit/fastqdump.config | 2 +-
src/nf_modules/UrQt/trimming_paired.config | 2 +-
src/nf_modules/UrQt/trimming_single.config | 2 +-
src/nf_modules/cutadapt/adaptor_removal_paired.config | 2 +-
src/nf_modules/cutadapt/adaptor_removal_single.config | 2 +-
src/nf_modules/cutadapt/trimming_paired.config | 2 +-
src/nf_modules/cutadapt/trimming_single.config | 2 +-
src/training_dataset.config | 4 ++--
21 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.config b/src/nf_modules/BEDtools/fasta_from_bed.config
index 6e19895..cae561d 100644
--- a/src/nf_modules/BEDtools/fasta_from_bed.config
+++ b/src/nf_modules/BEDtools/fasta_from_bed.config
@@ -13,7 +13,7 @@ profiles {
withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BEDtools/2.25.0"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 6611650..7f88967 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -12,7 +12,7 @@ profiles {
process{
withname: index_fasta {
beforeScript = "module purge; module load BWA/0.7.17"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index 68df48e..d9d7a82 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -12,7 +12,7 @@ profiles {
process{
withname: mapping_fastq {
beforeScript = "module purge; module load BWA/0.7.17"
- executor = "psmn"
+ executor = "sge"
cpus = 4
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
index 875a0fc..31b0daa 100644
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ b/src/nf_modules/FastQC/fastqc_paired.config
@@ -12,7 +12,7 @@ profiles {
process{
withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
index 875a0fc..31b0daa 100644
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ b/src/nf_modules/FastQC/fastqc_single.config
@@ -12,7 +12,7 @@ profiles {
process{
withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/Kallisto/indexing.config b/src/nf_modules/Kallisto/indexing.config
index 95d38d0..a76c54b 100644
--- a/src/nf_modules/Kallisto/indexing.config
+++ b/src/nf_modules/Kallisto/indexing.config
@@ -13,7 +13,7 @@ profiles {
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/Kallisto/mapping_paired.config b/src/nf_modules/Kallisto/mapping_paired.config
index 5200ee0..abd3b13 100644
--- a/src/nf_modules/Kallisto/mapping_paired.config
+++ b/src/nf_modules/Kallisto/mapping_paired.config
@@ -13,7 +13,7 @@ profiles {
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/Kallisto/mapping_single.config b/src/nf_modules/Kallisto/mapping_single.config
index 5200ee0..abd3b13 100644
--- a/src/nf_modules/Kallisto/mapping_single.config
+++ b/src/nf_modules/Kallisto/mapping_single.config
@@ -13,7 +13,7 @@ profiles {
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Kallisto/0.44.0"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
index f581bd0..57fed99 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ b/src/nf_modules/MUSIC/peak_calling_single.config
@@ -19,7 +19,7 @@ profiles {
withname: compute_mappability {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
@@ -28,7 +28,7 @@ profiles {
withname: music_preprocessing {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
@@ -37,7 +37,7 @@ profiles {
withname: music_computation {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MUSIC/6613c53"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
index 3b55ccc..fd3f433 100644
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ b/src/nf_modules/MultiQC/multiqc_paired.config
@@ -17,7 +17,7 @@ profiles {
withname: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
@@ -28,7 +28,7 @@ profiles {
withname: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MultiQC/1.0"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
index eff0320..786bbeb 100644
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ b/src/nf_modules/MultiQC/multiqc_single.config
@@ -16,7 +16,7 @@ profiles {
withname: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "FastQC/0.11.5"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
@@ -27,7 +27,7 @@ profiles {
withname: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "MultiQC/1.0"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config
index 30e5a2a..fe729b9 100644
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ b/src/nf_modules/RSEM/quantification_paired.config
@@ -13,7 +13,7 @@ profiles {
withname: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
index 30e5a2a..fe729b9 100644
--- a/src/nf_modules/RSEM/quantification_single.config
+++ b/src/nf_modules/RSEM/quantification_single.config
@@ -13,7 +13,7 @@ profiles {
withname: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "RSEM/1.3.0:SAMtools/1.7"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "30GB"
time = "24h"
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index 9fb28f9..d0e8273 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/src/nf_modules/SRAtoolkit/fastqdump.config
@@ -12,7 +12,7 @@ profiles {
process{
withname: fastq_dump {
beforeScript = "module purge; module load SRAtoolkit/2.8.2"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
index 59760a7..f11ad74 100644
--- a/src/nf_modules/UrQt/trimming_paired.config
+++ b/src/nf_modules/UrQt/trimming_paired.config
@@ -13,7 +13,7 @@ profiles {
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "UrQt/d62c1f8"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "5GB"
time = "12h"
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
index 59760a7..f11ad74 100644
--- a/src/nf_modules/UrQt/trimming_single.config
+++ b/src/nf_modules/UrQt/trimming_single.config
@@ -13,7 +13,7 @@ profiles {
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "UrQt/d62c1f8"
- executor = "psmn"
+ executor = "sge"
cpus = 16
memory = "5GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index ad9b4d2..dfc8600 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -13,7 +13,7 @@ profiles {
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index ad9b4d2..dfc8600 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -13,7 +13,7 @@ profiles {
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 6d5292d..82b2604 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -13,7 +13,7 @@ profiles {
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 6d5292d..82b2604 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -13,7 +13,7 @@ profiles {
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "cutadapt/1.14"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "20GB"
time = "12h"
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 3bddf5f..20f3db3 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -42,7 +42,7 @@ profiles {
process{
withname: build_synthetic_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
@@ -53,7 +53,7 @@ profiles {
}
withname: fasta_from_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
- executor = "psmn"
+ executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
--
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