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Merge pull request #363 from ramprasadn/feat/hasta_update

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Add a profile for stubruns in hasta
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Ramprasad Neethiraj 2022-08-23 22:14:18 +02:00 committed by GitHub
commit 49c71e0c28
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2 changed files with 28 additions and 5 deletions
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12
conf/hasta.config
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@ -25,10 +25,20 @@ process {
}
profiles {
dev_prio {
stub_prio {
params {
priority = 'development'
clusterOptions = "--qos=low"
max_memory = 6.GB
max_cpus = 1
max_time = 1.h
}
}
dev_prio {
params {
priority = 'development'
clusterOptions = "--qos=low"
}
}

13
conf/pipeline/raredisease/hasta.config
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@ -7,6 +7,19 @@ process {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
}
withLabel:'sentieon' {
beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
}
withName: 'BCFTOOLS_VIEW' {
if (params.genome == 'GRCh37') {
ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
} else if (params.genome == 'GRCh38') {
ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
}
publishDir = [
enabled: false,
]
}
// Java memory fixes
withName:'QUALIMAP_BAMQC' {