millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 00:26:03 +00:00
Code Issues Releases Packages Activity

Merge pull request #390 from raysloks/feat/hasta_java_memory_fix

Browse source 
Feat/hasta java memory fix
This commit is contained in:
Anders Jemt 2022-08-22 15:46:39 +02:00 committed by GitHub
commit 9c26cfddaa
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 7 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

8
conf/pipeline/raredisease/hasta.config
View file

@ -7,7 +7,13 @@ process {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
}
// Java memory fixes
withName:'QUALIMAP_BAMQC' {
ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
}
withName:'PICARD_MARKDUPLICATES' {
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
}
}