add sge config for some modules

src/nf_modules/BEDtools/bedtools.config

@@ -12,6 +12,14 @@ profiles {
     process{
       $fasta_from_bed {
         beforeScript = "module purge; module load BEDtools/2.25.0"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
       }
     }
   }

src/nf_modules/Kallisto/kallisto.config

@@ -15,9 +15,25 @@ profiles {
     process{
       $index_fasta {
         beforeScript = "module purge; module load Kallisto/0.43.1"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
       }
       $mapping_fastq {
         beforeScript = "module purge; module load Kallisto/0.43.1"
+        executor = "sge"
+        cpus = 4
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
       }
     }
   }

src/nf_modules/Kallisto/kallisto.nf

@@ -17,7 +17,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:

src/nf_modules/UrQt/urqt.config

@@ -12,6 +12,14 @@ profiles {
     process{
       $trimming {
         beforeScript = "module purge; module load UrQt/d62c1f8"
+        executor = "sge"
+        cpus = 4
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
       }
     }
   }

src/nf_modules/cutadapt/cutadapt.config

@@ -12,6 +12,14 @@ profiles {
     process{
       $adaptor_removal {
         beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
       }
     }
   }
@@ -31,6 +39,14 @@ profiles {
     process{
       $trimming {
         beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
       }
     }
   }