memory adjustments for samtools and MarkDuplicates

Author: Szilveszter Juhos

configuration/uppmax-localhost.config

@@ -70,9 +70,9 @@ process {
     memory = {params.totalMemory}
   }
   $MarkDuplicates {
-	// for deep sequencing we do need all the memory
+		// Actually the -Xmx value should be kept lower  
     cpus = 16
-    memory = {params.totalMemory}
+    memory = {2 * params.singleCPUMem}
   }
   $MergeBams {
     cpus = 16

configuration/uppmax-slurm.config

@@ -52,7 +52,9 @@ process {
     time = {params.runTime * task.attempt}
   }
   $MarkDuplicates {
-		// looks like overkill, but for deep sequencing we do need all the memory
+		// Actually the -Xmx value should be kept lower  
+    cpus = 16
+    memory = {2 * params.singleCPUMem}
   }
   $MergeBams {
     memory = {params.singleCPUMem * task.attempt}

main.nf

@@ -179,7 +179,7 @@ process MapReads {
   """
   bwa mem -R \"${readGroup}\" ${extra} -t ${task.cpus} -M \
   ${genomeFile} ${fastqFile1} ${fastqFile2} | \
-  samtools sort --threads ${task.cpus} -m 4G - > ${idRun}.bam
+  samtools sort --threads ${task.cpus} -m 2G - > ${idRun}.bam
   """
 }