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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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16
conf/hasta.config
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@ -16,19 +16,29 @@ singularity {
params { params {
max_memory = 180.GB max_memory = 180.GB
max_cpus = 36 max_cpus = 36
max_time = 336.h max_time = 336.h
} }
process { process {
executor = 'slurm' executor = 'slurm'
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }
} }
profiles { profiles {
dev_prio { stub_prio {
params { params {
priority = 'development' priority = 'development'
clusterOptions = "--qos=low" clusterOptions = "--qos=low"
max_memory = 6.GB
max_cpus = 1
max_time = 1.h
}
}
dev_prio {
params {
priority = 'development'
clusterOptions = "--qos=low"
} }
} }

17
conf/pipeline/raredisease/hasta.config
View file

@ -1,5 +1,5 @@
process { process {
withName:'PICARD_MARKDUPLICATES' { withName:'PICARD_MARKDUPLICATES' {
memory = { check_max( 90.GB * task.attempt, 'memory' ) } memory = { check_max( 90.GB * task.attempt, 'memory' ) }
} }
@ -7,6 +7,19 @@ process {
cpus = { check_max( 16 * task.attempt, 'cpus' ) } cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) } 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 // Java memory fixes
withName:'QUALIMAP_BAMQC' { withName:'QUALIMAP_BAMQC' {
@ -16,4 +29,4 @@ process {
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" } clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
} }
} }