memory adjustments for samtools and MarkDuplicates

SciLifeLab · Aug 14, 2018 · 393da8b · 393da8b
1 parent 98cf879
commit 393da8b
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/configuration/uppmax-localhost.config b/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

diff --git a/configuration/uppmax-slurm.config b/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}

diff --git a/main.nf b/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
   """
 }