From 5ef6d810e1b0368344afb6e4f6ef98113e8a008e Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 6 Mar 2021 14:58:54 +0100 Subject: [PATCH] Remove unnecesary picard -Xms flags --- main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index d45d92e9f..fd429efe4 100644 --- a/main.nf +++ b/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} """ }