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Resource Labels #647

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merged 7 commits into from
Jul 19, 2022
Merged

Resource Labels #647

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440d2f9
have freebayes only use a single core, parallel implementation isn't …
FriederikeHanssen Jul 17, 2022
9f6ee7b
resources that worked for matched ICGC WGS data
FriederikeHanssen Jul 19, 2022
1fcd53e
reduce resource requests in local modules
FriederikeHanssen Jul 19, 2022
e91c85b
fix naming
FriederikeHanssen Jul 19, 2022
ba1096a
update changelog
FriederikeHanssen Jul 19, 2022
e706b6b
merge upstream/dev
FriederikeHanssen Jul 19, 2022
c7c4d27
also add some docs on the resource requests
FriederikeHanssen Jul 19, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--snpeff_version` to allow more configuration on the snpeff container definition
- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--vep_include_fasta` to use the fasta file for annotation
- [#639](https://github.com/nf-core/sarek/pull/639) - Adding genes-txt-file and summary-html-file to the published output from snpEff.
- [#647](https://github.com/nf-core/sarek/pull/647) - Update resource requests for preprocessing based on what worked for 5 ICGC matched WGS samples
- [#652](https://github.com/nf-core/sarek/pull/652) - Added full size somatic test profile.

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24 changes: 22 additions & 2 deletions conf/base.config
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Expand Up @@ -49,8 +49,28 @@ process {
errorStrategy = 'retry'
maxRetries = 2
}
withName: 'BWAMEM2_MEM' {
memory = { check_max( 60.GB * task.attempt, 'memory' ) }
withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
cpus = { check_max( 24 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
time = { check_max( 48.h * task.attempt, 'time' ) }
}
withName: 'FASTP'{
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
}
withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT|SAMTOOLS_MERGE'{
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS'{
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{
memory = { check_max( 46.GB * task.attempt, 'memory' ) }
}
withName: 'GATK4_MARKDUPLICATES'{
memory = { check_max( 300.GB * task.attempt, 'memory' ) }
}
withName: 'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
}

}
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