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Revised base and all pipeline configs to provide memory on per core basis

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lquayle88 2022-10-04 09:12:29 +01:00
parent 3f2ffa314d
commit 584052cfff
5 changed files with 23 additions and 71 deletions
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20
conf/pipeline/atacseq/sbc_sharc.config
View file

@ -1,15 +1,5 @@
/* // Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // Custom Pipeline Resource Config for nf-core/atacseq
Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Custom Pipeline Resource Config for nf-core/atacseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// process-specific resource requirements - reduced specification from those in atacseq/conf/base.config // process-specific resource requirements - reduced specification from those in atacseq/conf/base.config
@ -25,19 +15,19 @@ process {
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 12.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( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 32.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( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 128.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

20
conf/pipeline/chipseq/sbc_sharc.config
View file

@ -1,15 +1,5 @@
/* // Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // Custom Pipeline Resource Config for nf-core/chipseq
Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Custom Pipeline Resource Config for nf-core/chipseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// process-specific resource requirements - reduced specification from those in chipseq/conf/base.config // process-specific resource requirements - reduced specification from those in chipseq/conf/base.config
@ -25,19 +15,19 @@ process {
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 12.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( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 32.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( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 128.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

22
conf/pipeline/rnaseq/sbc_sharc.config
View file

@ -1,15 +1,5 @@
/* // Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // Custom Pipeline Resource Config for nf-core/rnaseq
Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Custom Pipeline Resource Config for nf-core/rnaseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config // process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config
@ -25,19 +15,19 @@ process {
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 12.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( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 32.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( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 128.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -46,7 +36,7 @@ process {
} }
withLabel:process_high_memory { withLabel:process_high_memory {
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 160.GB * task.attempt, 'memory' ) }
} }
} }

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

@ -1,15 +1,5 @@
/* // Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // Custom Pipeline Resource Config for nf-core/sarek
Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Custom Pipeline Resource Config for nf-core/sarek
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// process-specific resource requirements - reduced specification from those in sarek/conf/base.config // process-specific resource requirements - reduced specification from those in sarek/conf/base.config
@ -77,7 +67,7 @@ process {
withName:'GATK4_MARKDUPLICATES' { withName:'GATK4_MARKDUPLICATES' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) } cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 240.GB * task.attempt, 'memory' ) } memory = { check_max( 240.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 12.h * task.attempt, 'time' ) }
} }
withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' { withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {

16
conf/sbc_sharc.config
View file

@ -1,14 +1,5 @@
/* // Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // Base Institutional Configuration
Sheffield Bioinformatics Core Configuration Profile - ShARC
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Base Institutional Configuration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// nf-core specific parameters displayed in header summary of each run // nf-core specific parameters displayed in header summary of each run
@ -42,7 +33,7 @@ process {
executor = 'sge' executor = 'sge'
penv = 'smp' penv = 'smp'
queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' } queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
clusterOptions = { "-l rmem=${task.memory.toGiga()/task.cpus}G" } clusterOptions = { "-l rmem=${ (task.memory.toGiga() / task.cpus) }G" }
} }
@ -65,3 +56,4 @@ singularity {
autoMounts = true autoMounts = true
} }