cutadapt: update nf config files for the PSMN

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -3,23 +3,21 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $adaptor_removal {
+      withName: adaptor_removal {
         container = "cutadapt:1.14"
       }
     }
   }
   sge {
     process{
-      $adaptor_removal {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: adaptor_removal {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -3,23 +3,21 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $adaptor_removal {
+      withName: adaptor_removal {
         container = "cutadapt:1.14"
       }
     }
   }
   sge {
     process{
-      $adaptor_removal {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: adaptor_removal {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }

src/nf_modules/cutadapt/trimming_paired.config

@@ -3,23 +3,21 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $trimming {
+      withName: trimming {
         container = "cutadapt:1.14"
       }
     }
   }
   sge {
     process{
-      $trimming {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }

src/nf_modules/cutadapt/trimming_single.config

@@ -3,23 +3,21 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $trimming {
+      withName: trimming {
         container = "cutadapt:1.14"
       }
     }
   }
   sge {
     process{
-      $trimming {
-        beforeScript = "module purge; module load cutadapt/1.14"
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
         executor = "sge"
         cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }