UrQt: switch cpus config from .nf to .config

src/nf_modules/UrQt/trimming_paired.config

@@ -4,6 +4,7 @@ profiles {
     docker.enabled = true
     process {
       withName: trimming {
+        cpus = 4
         container = "urqt:d62c1f8"
       }
     }
@@ -12,6 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: trimming {
+        cpus = 4
         container = "file:///bin/UrQt:d62c1f8.sif"
       }
     }
@@ -24,6 +26,7 @@ profiles {
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "5GB"
+        cpus = 16
         time = "12h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
         penv = 'openmp16'

src/nf_modules/UrQt/trimming_paired.nf

@@ -7,7 +7,6 @@ Channel
 
 process trimming {
   tag "${reads}"
-  cpus 4
   publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:

src/nf_modules/UrQt/trimming_single.config

@@ -5,6 +5,7 @@ profiles {
     process {
       withName: trimming {
         container = "urqt:d62c1f8"
+        cpus = 4
       }
     }
   }
@@ -13,6 +14,7 @@ profiles {
     process {
       withName: trimming {
         container = "file:///bin/UrQt:d62c1f8.sif"
+        cpus = 4
       }
     }
   }
@@ -23,6 +25,7 @@ profiles {
         module = "UrQt/d62c1f8"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "5GB"
         time = "12h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'

src/nf_modules/UrQt/trimming_single.nf

@@ -10,7 +10,7 @@ Channel
 
 process trimming {
   tag "$file_id"
-  cpus 4
+  echo true
 
   input:
   set file_id, file(reads) from fastq_files