nf config: rename sge to psmn

src/nf_modules/RSEM/indexing.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $index_fasta {
         beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"

src/nf_modules/RSEM/quantification_paired.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $mapping_fastq {
         beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"

src/nf_modules/RSEM/quantification_single.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $mapping_fastq {
         beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"

src/nf_modules/SAMtools/filter_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $filter_bam {
         beforeScript = "module purge; module load SAMtools/1.7"

src/nf_modules/SAMtools/index_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $index_bam {
         beforeScript = "module purge; module load SAMtools/1.7"

src/nf_modules/SAMtools/sort_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $sort_bam {
         beforeScript = "module purge; module load SAMtools/1.7"

src/nf_modules/SAMtools/split_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $split_bam {
         beforeScript = "module purge; module load SAMtools/1.7"

src/nf_modules/SRAtoolkit/fastqdump.config

@@ -8,11 +8,11 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $fastq_dump {
         beforeScript = "module purge; module load SRAtoolkit/2.8.2"
-        executor = "sge"
+        executor = "psmn"
         cpus = 1
         memory = "5GB"
         time = "6h"

src/nf_modules/UrQt/trimming_paired.config

@@ -8,12 +8,12 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "UrQt/d62c1f8"
-        executor = "sge"
+        executor = "psmn"
         cpus = 16
         memory = "5GB"
         time = "12h"

src/nf_modules/UrQt/trimming_single.config

@@ -8,12 +8,12 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "UrQt/d62c1f8"
-        executor = "sge"
+        executor = "psmn"
         cpus = 16
         memory = "5GB"
         time = "12h"

src/nf_modules/UrQt/urqt.config

@@ -8,11 +8,11 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $trimming {
         beforeScript = "module purge; module load UrQt/d62c1f8"
-        executor = "sge"
+        executor = "psmn"
         cpus = 4
         memory = "5GB"
         time = "6h"

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -8,12 +8,12 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       withName: adaptor_removal {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "cutadapt/1.14"
-        executor = "sge"
+        executor = "psmn"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -8,12 +8,12 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       withName: adaptor_removal {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "cutadapt/1.14"
-        executor = "sge"
+        executor = "psmn"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/cutadapt/trimming_paired.config

@@ -8,12 +8,12 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "cutadapt/1.14"
-        executor = "sge"
+        executor = "psmn"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/cutadapt/trimming_single.config

@@ -8,12 +8,12 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "cutadapt/1.14"
-        executor = "sge"
+        executor = "psmn"
         cpus = 1
         memory = "20GB"
         time = "12h"

src/nf_modules/sambamba/index_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $index_bam {
         beforeScript = "module purge; module load sambamba/0.6.7"

src/nf_modules/sambamba/sort_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $sort_bam {
         beforeScript = "module purge; module load sambamba/0.6.7"

src/nf_modules/sambamba/split_bams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $split_bam {
         beforeScript = "module purge; module load sambamba/0.6.7"

src/nf_modules/samblaster/dedup_sams.config

@@ -8,7 +8,7 @@ profiles {
       }
     }
   }
-  sge {
+  psmn {
     process{
       $dedup_sam {
         beforeScript = "module purge; module load samblaster/0.1.24"