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

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master
lquayle88 2 years ago
parent 3f2ffa314d
commit 584052cfff
5 changed files with 23 additions and 71 deletions
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20
conf/pipeline/atacseq/sbc_sharc.config
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@ -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
@ -25,19 +15,19 @@ process {
withLabel:process_low {
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' ) }
}
withLabel:process_medium {
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' ) }
}
withLabel:process_high {
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' ) }
}

20
conf/pipeline/chipseq/sbc_sharc.config
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@ -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
@ -25,19 +15,19 @@ process {
withLabel:process_low {
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' ) }
}
withLabel:process_medium {
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' ) }
}
withLabel:process_high {
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' ) }
}

22
conf/pipeline/rnaseq/sbc_sharc.config
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@ -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
@ -25,19 +15,19 @@ process {
withLabel:process_low {
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' ) }
}
withLabel:process_medium {
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' ) }
}
withLabel:process_high {
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' ) }
}
@ -46,7 +36,7 @@ process {
}
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
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@ -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
@ -77,7 +67,7 @@ process {
withName:'GATK4_MARKDUPLICATES' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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' {

16
conf/sbc_sharc.config
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@ -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
@ -42,7 +33,7 @@ process {
executor = 'sge'
penv = 'smp'
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
}

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