Merge pull request #689 from nf-core/remove-xms

Remove left-over picard -Xms java flags

Author: jfy133

main.nf

@@ -964,7 +964,7 @@ process makeSeqDict {
 
     script:
     """
-    picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M CreateSequenceDictionary R=$fasta O="${fasta.baseName}.dict"
+    picard -Xmx${task.memory.toMega()}M CreateSequenceDictionary R=$fasta O="${fasta.baseName}.dict"
     """
 }
 
@@ -2166,12 +2166,12 @@ process markduplicates{
     // To make sure direct BAMs have a clean name
     """
     mv ${bam} ${libraryid}.bam
-    picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M MarkDuplicates INPUT=${libraryid}.bam OUTPUT=${libraryid}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${libraryid}_rmdup.metrics" VALIDATION_STRINGENCY=SILENT
+    picard -Xmx${task.memory.toMega()}M MarkDuplicates INPUT=${libraryid}.bam OUTPUT=${libraryid}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${libraryid}_rmdup.metrics" VALIDATION_STRINGENCY=SILENT
     samtools index ${libraryid}_rmdup.bam ${size}
     """
     } else {
     """
-    picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M MarkDuplicates INPUT=${libraryid}.bam OUTPUT=${libraryid}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${libraryid}_rmdup.metrics" VALIDATION_STRINGENCY=SILENT
+    picard -Xmx${task.memory.toMega()}M MarkDuplicates INPUT=${libraryid}.bam OUTPUT=${libraryid}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${libraryid}_rmdup.metrics" VALIDATION_STRINGENCY=SILENT
     samtools index ${libraryid}_rmdup.bam ${size}
     """
     }