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Improve memory and error handling of qualimap #630

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Merged
jfy133 merged 3 commits into from
Dec 11, 2020
Merged

Improve memory and error handling of qualimap #630

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9b867cd
improve memory and error hadnling of qualimap
maxibor Dec 10, 2020
e07e7b5
missing = sign
maxibor Dec 10, 2020
96135fe
update changelog
maxibor Dec 10, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- Removed leftover old DockerHub push CI commands.
- [#627](https://github.com/nf-core/eager/issues/627) Added de Barros Damgaard citation to README
- [#630](https://github.com/nf-core/eager/pull/630) Better handling of Qualimap memory requirements and error strategy.

### `Dependencies`

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2 changes: 1 addition & 1 deletion conf/base.config
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Expand Up @@ -74,7 +74,7 @@ process {
}

withName:qualimap{
errorStrategy = 'ignore'
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
}

withName:preseq {
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -2443,7 +2443,7 @@ process qualimap {
script:
def snpcap = params.snpcapture_bed != '' ? "-gff ${params.snpcapture_bed}" : ''
"""
qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap}
qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap} --java-mem-size=${task.memory.toGiga()}G
"""
}

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