Added other Java processes with memory overhead, sorted alphabetically

conf/pipeline/sarek/eddie.config

@@ -1,59 +1,77 @@
 process {
-
-  withName:BWAMEM_MEM {
-    cpus = 16
-    memory = 128.GB
-    clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
+  withName:APPLYBQSR {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:APPLYBQSR_SPARK {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_APPLYVQSR {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_BASERECALIBRATOR {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_BASERECALIBRATOR_SPARK {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_CALCULATECONTAMINATION {  
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_CNNSCOREVARIANTS {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
   withName:GATK4_CREATESEQUENCEDICTIONARY {
-    cpus = 1
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:LEARNREADORIENTATIONMODEL {
+  withName:GATK4_ESTIMATELIBRARYCOMPLEXITY {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:QUALIMAP_BAMQC {
-    cpus = 8
-    memory = 128.GB
-    clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
+  withName:GATK4_FILTERMUTECTCALLS {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GATK4_MARKDUPLICATES {
+  withName:GATK4_FILTERVARIANTTRANCHES {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:BASERECALIBRATOR {
+  withName:GATK4_GATHERBQSRREPORTS {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:APPLYBQSR {
+  withName:GATK4_GATHERPILEUPSUMMARIES {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_GENOMICSDBIMPORT {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GATHERBQSRREPORTS {
+  withName:GATK4_GENOTYPEGVCFS {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_GETPILEUPSUMMARIES {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
   withName:GATK4_HAPLOTYPECALLER {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GATK4_GENOTYPEGVCFS {
+  withName:GATK4_INTERVALLISTTOBED {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:MUTECT2 {
+  withName:GATK4_LEARNREADORIENTATIONMODEL {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:MERGE_MUTECT2 {
+  withName:GATK4_MARKDUPLICATES {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:MERGEMUTECTSTATS {
+  withName:GATK4_MARKDUPLICATES_SPARK {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GETPILEUPSUMMARIES {
+  withName:GATK4_MERGEMUTECTSTATS {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GATHERPILEUPSUMMARIES {
+  withName:GATK4_MERGEVCFS {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:CALCULATECONTAMINATION {  
+  withName:GATK4_MUTECT2 {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:FILTERMUTECTCALLS {
+  withName:GATK4_VARIANTRECALIBRATOR {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
-  }  
+  }
 }