mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-09-21 06:02:03 +00:00
42 lines
1.5 KiB
Text
42 lines
1.5 KiB
Text
// Profile config names for nf-core/configs
|
|
|
|
params {
|
|
// Specific nf-core/configs params
|
|
config_profile_contact = 'Friederike Hanssen (@FriederikeHanssen)'
|
|
config_profile_description = 'nf-core/sarek CFC profile provided by nf-core/configs'
|
|
}
|
|
|
|
// Specific nf-core/sarek process configuration
|
|
process {
|
|
withName:'StrelkaSingle|Strelka|StrelkaBP|MantaSingle|Manta' {
|
|
cpus = { check_resource( 20 * task.attempt) }
|
|
memory = { check_resource( 59.GB * task.attempt) }
|
|
}
|
|
withName:'MSIsensor_scan|MSIsensor_msi' {
|
|
memory = { check_resource( 55.GB * task.attempt ) }
|
|
|
|
}
|
|
withName:BamQC {
|
|
memory = { check_resource( 372.GB * task.attempt) }
|
|
}
|
|
|
|
withName:MapReads{
|
|
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"
|
|
}
|
|
}
|