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include stub profile

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This commit is contained in:
Ramprasad Neethiraj 2022-04-15 15:27:41 +02:00
parent e9d93d62e0
commit afe935c2d0
2 changed files with 38 additions and 5 deletions
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22
conf/hasta.config
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@ -15,19 +15,35 @@ 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 ?: ''}" }
}
params {
max_memory = 180.GB
max_cpus = 36
max_time = 336.h
} }
profiles { profiles {
dev_prio { stub_prio {
params { params {
priority = 'development' priority = 'development'
clusterOptions = "--qos=low" clusterOptions = "--qos=low"
max_memory = 1.GB
max_cpus = 1
max_time = 1.h
}
}
dev_prio {
params {
priority = 'development'
clusterOptions = "--qos=low"
} }
} }

21
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' ) }
} }
@ -7,4 +7,21 @@ 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' ) }
} }
} withname: BCFTOOLS_VIEW {
if (params.genome == 'GRCh37') {
ext.args = '--output-type v --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 v --apply-filters PASS --exclude "INFO/swegenAF > 0.40"'
}
publishDir = [
enabled: false,
]
}
}
params {
sentieon_install_dir = '/home/proj/bin/sentieon/sentieon-genomics-202010.02/bin'
}