millironx/nf-configs
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Code Issues Releases Packages Activity

Updated resource requests for compatibility with general worker nodes

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lquayle88 2022-09-23 11:08:39 +01:00
parent 1471257aaf
commit 7e34beb3c9
4 changed files with 8 additions and 12 deletions
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2
conf/pipeline/atacseq/sbc_sharc.config
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@ -37,7 +37,7 @@ process {
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

2
conf/pipeline/chipseq/sbc_sharc.config
View file

@ -37,7 +37,7 @@ process {
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

6
conf/pipeline/rnaseq/sbc_sharc.config
View file

@ -37,7 +37,7 @@ process {
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -45,10 +45,6 @@ process {
time = { check_max( 12.h * task.attempt, 'time' ) } time = { check_max( 12.h * task.attempt, 'time' ) }
} }
withLabel:process_high_memory {
memory = { check_max( 60.GB * task.attempt, 'memory' ) }
}
} }

10
conf/pipeline/sarek/sbc_sharc.config
View file

@ -37,7 +37,7 @@ process {
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -46,7 +46,7 @@ process {
} }
withLabel:process_high_memory { withLabel:process_high_memory {
memory = { check_max( 60.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
} }
@ -54,7 +54,7 @@ process {
withName:'BWAMEM1_MEM|BWAMEM2_MEM' { withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) } cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -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( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
} }
withName:'GATK4_MARKDUPLICATES' { withName:'GATK4_MARKDUPLICATES' {
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) }
} }
withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' { withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {