add clusterOption for psmn to all config files

src/nf_modules/BEDtools/fasta_from_bed.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "BEDtools/2.25.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/BWA/indexing.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "BWA/0.7.17"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "30GB"
         time = "12h"

src/nf_modules/BWA/mapping_paired.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "BWA/0.7.17"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Bowtie/indexing.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie/1.2.2"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/Bowtie/mapping_paired.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie/1.2.2:SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Bowtie/mapping_single.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie/1.2.2:SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Bowtie2/indexing.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Bowtie2/mapping_paired.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1:SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Bowtie2/mapping_single.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1:SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/FastQC/fastqc_paired.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/FastQC/fastqc_single.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/HTSeq/htseq.config

@@ -17,6 +17,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
@@ -26,6 +27,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "HTSeq/0.8.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/Kallisto/indexing.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Kallisto/0.44.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Kallisto/mapping_paired.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Kallisto/0.44.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/Kallisto/mapping_single.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Kallisto/0.44.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/MUSIC/peak_calling_single.config

@@ -20,6 +20,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MUSIC/6613c53"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
@@ -29,6 +30,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MUSIC/6613c53"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"
@@ -38,6 +40,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MUSIC/6613c53"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/MultiQC/multiqc_paired.config

@@ -18,6 +18,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "5GB"
         time = "6h"
@@ -29,6 +30,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MultiQC/1.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "5GB"
         time = "6h"

src/nf_modules/MultiQC/multiqc_single.config

@@ -17,6 +17,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "5GB"
         time = "6h"
@@ -28,6 +29,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MultiQC/1.0"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 1
         memory = "5GB"
         time = "6h"

src/nf_modules/RSEM/indexing.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "RSEM/1.3.0:SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"

src/nf_modules/RSEM/quantification_paired.config

@@ -14,6 +14,7 @@ profiles {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "RSEM/1.3.0:SAMtools/1.7"
         executor = "sge"
+        clusterOptions = "-m e -cwd -V"
         cpus = 16
         memory = "30GB"
         time = "24h"