diff --git a/conf/pipeline/atacseq/sbc_sharc.config b/conf/pipeline/atacseq/sbc_sharc.config index 97cd758..60cbc49 100644 --- a/conf/pipeline/atacseq/sbc_sharc.config +++ b/conf/pipeline/atacseq/sbc_sharc.config @@ -24,20 +24,20 @@ process { // process labels withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 4.GB * task.attempt, 'memory' ) } + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { - cpus = { check_max( 4 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } + cpus = { check_max( 10 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_high { - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + cpus = { check_max( 15 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } diff --git a/conf/pipeline/chipseq/sbc_sharc.config b/conf/pipeline/chipseq/sbc_sharc.config index a2f6431..10de65b 100644 --- a/conf/pipeline/chipseq/sbc_sharc.config +++ b/conf/pipeline/chipseq/sbc_sharc.config @@ -24,20 +24,20 @@ process { // process labels withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 4.GB * task.attempt, 'memory' ) } + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { - cpus = { check_max( 4 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } + cpus = { check_max( 10 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_high { - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + cpus = { check_max( 15 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } diff --git a/conf/pipeline/rnaseq/sbc_sharc.config b/conf/pipeline/rnaseq/sbc_sharc.config index 8f905f7..fe50bc6 100644 --- a/conf/pipeline/rnaseq/sbc_sharc.config +++ b/conf/pipeline/rnaseq/sbc_sharc.config @@ -24,20 +24,20 @@ process { // process labels withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 4.GB * task.attempt, 'memory' ) } + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { - cpus = { check_max( 4 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } + cpus = { check_max( 10 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_high { - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + cpus = { check_max( 15 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } @@ -45,6 +45,10 @@ process { time = { check_max( 12.h * task.attempt, 'time' ) } } + withLabel:process_high_memory { + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + } + } diff --git a/conf/pipeline/sarek/sbc_sharc.config b/conf/pipeline/sarek/sbc_sharc.config index 24312a7..75e2be0 100644 --- a/conf/pipeline/sarek/sbc_sharc.config +++ b/conf/pipeline/sarek/sbc_sharc.config @@ -24,20 +24,20 @@ process { // process labels withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 4.GB * task.attempt, 'memory' ) } + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { - cpus = { check_max( 4 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } + cpus = { check_max( 10 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_high { - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + cpus = { check_max( 15 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } @@ -46,20 +46,20 @@ process { } withLabel:process_high_memory { - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } } // process name withName:'BWAMEM1_MEM|BWAMEM2_MEM' { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } + cpus = { check_max( 15 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } withName:'FASTP' { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } + cpus = { check_max( 15 * task.attempt, 'cpus' ) } } withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT' { @@ -71,11 +71,11 @@ process { } withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' { - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } } withName:'GATK4_MARKDUPLICATES' { - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } } withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' { diff --git a/conf/sbc_sharc.config b/conf/sbc_sharc.config index a8a096e..21dd18b 100644 --- a/conf/sbc_sharc.config +++ b/conf/sbc_sharc.config @@ -27,7 +27,7 @@ params { params { max_cpus = 16 - max_memory = 64.GB + max_memory = 256.GB max_time = 96.h } @@ -52,7 +52,7 @@ process { executor { queueSize = 10 - submitRateLimit = '12/1min' + submitRateLimit = '1 sec' }