mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
Add check_resource to respect max_resource/max_cpus
This commit is contained in:
parent
8e554cd43c
commit
f6e16f2872
1 changed files with 23 additions and 6 deletions
|
@ -9,17 +9,34 @@ params {
|
|||
// Specific nf-core/sarek process configuration
|
||||
process {
|
||||
withName:'StrelkaSingle|Strelka|StrelkaBP|MantaSingle|Manta' {
|
||||
memory = 59.GB
|
||||
cpus = 20
|
||||
cpus = { check_resource( 20 * task.attempt) }
|
||||
memory = { check_resource( 59.GB * task.attempt) }
|
||||
}
|
||||
withName:'MSIsensor_scan|MSIsensor_msi' {
|
||||
memory = 55.GB
|
||||
memory = { check_resource( 55.GB * task.attempt ) }
|
||||
|
||||
}
|
||||
withName:BamQC {
|
||||
memory = 372.GB
|
||||
memory = { check_resource( 372.GB * task.attempt) }
|
||||
}
|
||||
|
||||
withName:MapReads{
|
||||
cpus = 20
|
||||
memory = 59.GB
|
||||
cpus = { check_resource( 20 * task.attempt ) }
|
||||
memory = { check_resource( 59.GB * task.attempt) }
|
||||
}
|
||||
}
|
||||
|
||||
def check_resource(obj) {
|
||||
try {
|
||||
if (obj.getClass() == nextflow.util.MemoryUnit && obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
|
||||
return params.max_memory as nextflow.util.MemoryUnit
|
||||
else if (obj.getClass() == nextflow.util.Duration && obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
|
||||
return params.max_time as nextflow.util.Duration
|
||||
else if (obj.getClass() == java.lang.Integer)
|
||||
return Math.min(obj, params.max_cpus as int)
|
||||
else
|
||||
return obj
|
||||
} catch (all) {
|
||||
println " ### ERROR ### Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}' is not valid! Using default value: $obj"
|
||||
}
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue