Kallisto: update nf config for PSMN

src/nf_modules/Kallisto/indexing.config

@@ -3,24 +3,25 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
+      withName: index_fasta {
         container = "kallisto:0.44.0"
       }
     }
   }
   sge {
     process{
-      $index_fasta {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
         executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }
 }
+
+

src/nf_modules/Kallisto/mapping_paired.config

@@ -3,24 +3,25 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withName: mapping_fastq {
         container = "kallisto:0.44.0"
       }
     }
   }
   sge {
     process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
         executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }
 }
+
+

src/nf_modules/Kallisto/mapping_single.config

@@ -3,24 +3,25 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withName: mapping_fastq {
         container = "kallisto:0.44.0"
       }
     }
   }
   sge {
     process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
         executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }
 }
+
+