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Remove left-over picard -Xms java flags #689

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Merged
jfy133 merged 1 commit into from
Mar 6, 2021
Merged

Remove left-over picard -Xms java flags #689

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6 changes: 3 additions & 3 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
"""
}

Expand Down Expand Up @@ -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}
"""
}
Expand Down
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