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Fix picard memory issue #145

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merged 1 commit into from
Feb 19, 2019
Merged

Fix picard memory issue #145

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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

## [Unpublished / Dev Branch]

### `Added`

### `Fixed`
* [#145](https://github.com/nf-core/eager/issues/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144)


## [2.0.5] - 2019-01-28

### `Added`
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5 changes: 4 additions & 1 deletion conf/base.config
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Expand Up @@ -31,7 +31,10 @@ process {
withName:convertBam {
cpus = { check_max(8 * task.attempt, 'cpus') }
}

withName:makeSeqDict {
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
}

withName:bwa {
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
cpus = { check_max(8 * task.attempt, 'cpus') }
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4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -488,7 +488,7 @@ process makeSeqDict {
mkdir -p seq_dict
mv $fasta "seq_dict/${base}"
cd seq_dict
picard CreateSequenceDictionary R=$base O="${fasta.baseName}.dict"
picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M CreateSequenceDictionary R=$base O="${fasta.baseName}.dict"
"""
}

Expand Down Expand Up @@ -970,7 +970,7 @@ process markDup{
script:
prefix = "${bam.baseName}"
"""
picard MarkDuplicates INPUT=$bam OUTPUT=${prefix}.markDup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${prefix}.markdup.metrics" VALIDATION_STRINGENCY=SILENT
picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M MarkDuplicates INPUT=$bam OUTPUT=${prefix}.markDup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${prefix}.markdup.metrics" VALIDATION_STRINGENCY=SILENT
"""
}

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