millironx/nf-configs
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Code Issues Releases Packages Activity

Updated resource requests for compatibility with high memory nodes

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lquayle88 2022-09-23 13:18:50 +01:00
parent 7541ffb666
commit ab1ad832df
5 changed files with 36 additions and 32 deletions
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12
conf/pipeline/atacseq/sbc_sharc.config
View file

@ -24,20 +24,20 @@ process {
// process labels // process labels
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) } time = { check_max( 4.h * task.attempt, 'time' ) }
} }
withLabel:process_medium { withLabel:process_medium {
cpus = { check_max( 4 * task.attempt, 'cpus' ) } cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) } time = { check_max( 6.h * task.attempt, 'time' ) }
} }
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 15 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

12
conf/pipeline/chipseq/sbc_sharc.config
View file

@ -24,20 +24,20 @@ process {
// process labels // process labels
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) } time = { check_max( 4.h * task.attempt, 'time' ) }
} }
withLabel:process_medium { withLabel:process_medium {
cpus = { check_max( 4 * task.attempt, 'cpus' ) } cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) } time = { check_max( 6.h * task.attempt, 'time' ) }
} }
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 15 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

16
conf/pipeline/rnaseq/sbc_sharc.config
View file

@ -24,20 +24,20 @@ process {
// process labels // process labels
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) } time = { check_max( 4.h * task.attempt, 'time' ) }
} }
withLabel:process_medium { withLabel:process_medium {
cpus = { check_max( 4 * task.attempt, 'cpus' ) } cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) } time = { check_max( 6.h * task.attempt, 'time' ) }
} }
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 15 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -45,6 +45,10 @@ process {
time = { check_max( 12.h * task.attempt, 'time' ) } time = { check_max( 12.h * task.attempt, 'time' ) }
} }
withLabel:process_high_memory {
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
}
} }

24
conf/pipeline/sarek/sbc_sharc.config
View file

@ -24,20 +24,20 @@ process {
// process labels // process labels
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) } time = { check_max( 4.h * task.attempt, 'time' ) }
} }
withLabel:process_medium { withLabel:process_medium {
cpus = { check_max( 4 * task.attempt, 'cpus' ) } cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) } time = { check_max( 6.h * task.attempt, 'time' ) }
} }
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 15 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -46,20 +46,20 @@ process {
} }
withLabel:process_high_memory { withLabel:process_high_memory {
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
} }
// process name // process name
withName:'BWAMEM1_MEM|BWAMEM2_MEM' { withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) } cpus = { check_max( 15 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
withName:'FASTP' { withName:'FASTP' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) } cpus = { check_max( 15 * task.attempt, 'cpus' ) }
} }
withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT' { withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT' {
@ -71,11 +71,11 @@ process {
} }
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' { 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' { 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' { withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {

4
conf/sbc_sharc.config
View file

@ -27,7 +27,7 @@ params {
params { params {
max_cpus = 16 max_cpus = 16
max_memory = 64.GB max_memory = 256.GB
max_time = 96.h max_time = 96.h
} }
@ -52,7 +52,7 @@ process {
executor { executor {
queueSize = 10 queueSize = 10
submitRateLimit = '12/1min' submitRateLimit = '1 sec'
} }