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add speed up parameters for genomicsdb #827

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Nov 11, 2022
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add speed up parameters for genomicsdb #827

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1729642
add speed up parameters for genomicsdb
FriederikeHanssen Nov 10, 2022
77e756f
update changelog
FriederikeHanssen Nov 10, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#806](https://github.com/nf-core/sarek/pull/806) - Split up `modules.config` file
- [#810](https://github.com/nf-core/sarek/pull/810) - Update CHANGELOG
- [#821](https://github.com/nf-core/sarek/pull/821) - Change `replace` to `putIfAbsent` for automatic search of `input` if none is provided to avoid overwriting values
- [#827](https://github.com/nf-core/sarek/pull/827) - Add `--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader` to `GenomicsDB` parameters to speed up the analysis

### Fixed

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1 change: 1 addition & 0 deletions conf/modules/haplotypecaller.config
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Expand Up @@ -55,6 +55,7 @@ process {
}

withName: 'GATK4_GENOMICSDBIMPORT' {
ext.args = { "--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader "}
ext.prefix = { meta.num_intervals > 1 ? "${meta.intervals_name}.joint" : "joint" }
ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline && !params.no_intervals}
}
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