nf module: update executor from psmn to sge

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"

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"