diff --git a/conf/pipeline/sarek/sbc_sharc.config b/conf/pipeline/sarek/sbc_sharc.config index d970574..4ef0534 100644 --- a/conf/pipeline/sarek/sbc_sharc.config +++ b/conf/pipeline/sarek/sbc_sharc.config @@ -25,19 +25,19 @@ process { withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + memory = { check_max( 72.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_high { cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + memory = { check_max( 192.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } @@ -46,7 +46,7 @@ process { } withLabel:process_high_memory { - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + memory = { check_max( 240.GB * task.attempt, 'memory' ) } } @@ -54,7 +54,7 @@ process { withName:'BWAMEM1_MEM|BWAMEM2_MEM' { cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + memory = { check_max( 192.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } @@ -71,12 +71,12 @@ process { } withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' { - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + memory = { check_max( 72.GB * task.attempt, 'memory' ) } } withName:'GATK4_MARKDUPLICATES' { - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + cpus = { check_max( 12 * task.attempt, 'cpus' ) } + memory = { check_max( 240.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } diff --git a/conf/sbc_sharc.config b/conf/sbc_sharc.config index 21dd18b..6583da7 100644 --- a/conf/sbc_sharc.config +++ b/conf/sbc_sharc.config @@ -42,7 +42,7 @@ process { executor = 'sge' penv = 'smp' queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' } - clusterOptions = { "-l rmem=${task.memory.toGiga()}G" } + clusterOptions = { "-l rmem=${task.memory.toGiga()/task.cpus}G" } }