Leave some spare memory for samtools. See nf-core#81

main.nf

@@ -666,10 +666,11 @@ if( params.aligner == 'bwameth' ){
         file "where_are_my_files.txt"
 
         script:
+        def avail_mem = task.memory ? (task.memory.toBytes() - 6000000000) / task.cpus) : false
+        def sort_mem = avail_mem && avail_mem > 2000000000 ? "-m $avail_mem" : ''
         """
         samtools sort $bam \\
-            -m ${task.memory.toBytes() / task.cpus} \\
-            -@ ${task.cpus} \\
+            -@ ${task.cpus} $sort_mem \\
             -o ${bam.baseName}.sorted.bam
         samtools index ${bam.baseName}.sorted.bam
         samtools flagstat ${bam.baseName}.sorted.bam > ${bam.baseName}_flagstat_report.txt
@@ -770,10 +771,11 @@ process qualimap {
     script:
     gcref = params.genome == 'GRCh37' ? '-gd HUMAN' : ''
     gcref = params.genome == 'GRCm38' ? '-gd MOUSE' : ''
+    def avail_mem = task.memory ? (task.memory.toBytes() - 6000000000) / task.cpus) : false
+    def sort_mem = avail_mem && avail_mem > 2000000000 ? "-m $avail_mem" : ''
     """
     samtools sort $bam \\
-        -m ${task.memory.toBytes() / task.cpus} \\
-        -@ ${task.cpus} \\
+        -@ ${task.cpus} $sort_mem \\
         -o ${bam.baseName}.sorted.bam
     qualimap bamqc $gcref \\
         -bam ${bam.baseName}.sorted.bam \\
@@ -798,10 +800,11 @@ process preseq {
     file "${bam.baseName}.ccurve.txt" into preseq_results
 
     script:
+    def avail_mem = task.memory ? (task.memory.toBytes() - 6000000000) / task.cpus) : false
+    def sort_mem = avail_mem && avail_mem > 2000000000 ? "-m $avail_mem" : ''
     """
     samtools sort $bam \\
-        -m ${task.memory.toBytes() / task.cpus} \\
-        -@ ${task.cpus} \\
+        -@ ${task.cpus} $sort_mem \\
         -o ${bam.baseName}.sorted.bam
     preseq lc_extrap -v -B ${bam.baseName}.sorted.bam -o ${bam.baseName}.ccurve.txt
     """