Remove hardcoded ARFiXPrefix memory as issue was SGE/JAVA specific

Author: jfy133

main.nf

@@ -1176,7 +1176,7 @@ process adapter_removal {
     mv *.settings output/
 
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx500m output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
 
     pigz -p ${task.cpus} output/${base}.pe.combined.fq
     """
@@ -1192,7 +1192,7 @@ process adapter_removal {
     mv *.settings output/
 
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx500m output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
 
     pigz -p ${task.cpus} output/${base}.pe.combined.fq
     """
@@ -1205,7 +1205,7 @@ process adapter_removal {
     cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
         
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx500m output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
     
     pigz -p ${task.cpus} output/${base}.pe.combined.fq
 
@@ -1220,7 +1220,7 @@ process adapter_removal {
     cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
     
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx500m  output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g  output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
     
     pigz -p ${task.cpus} output/${base}.pe.combined.fq
 
@@ -1236,7 +1236,7 @@ process adapter_removal {
     cat *.collapsed.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
         
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx500m output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
     
     pigz -p ${task.cpus} output/${base}.pe.combined.fq
 
@@ -1252,7 +1252,7 @@ process adapter_removal {
     cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
     
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx500m output/${base}.pe.combined.tmp.fq.gz  > output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz  > output/${base}.pe.combined.fq
     
     pigz -p ${task.cpus} output/${base}.pe.combined.fq