millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-12-22 10:38:16 +00:00
Code Issues Releases Packages Activity

Merge pull request #286 from FriederikeHanssen/cfc

Browse source 
Update sarek - cfc specific config
This commit is contained in:
FriederikeHanssen 2021-10-05 10:50:08 +02:00 committed by GitHub
commit 4f8b0d6478
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 23 additions and 6 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

29
conf/pipeline/sarek/cfc.config
View file

@ -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"
}
}