diff --git a/conf/pipeline/atacseq/sbc_sharc.config b/conf/pipeline/atacseq/sbc_sharc.config index 0660591..7cd0e4a 100644 --- a/conf/pipeline/atacseq/sbc_sharc.config +++ b/conf/pipeline/atacseq/sbc_sharc.config @@ -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' ) } } diff --git a/conf/pipeline/chipseq/sbc_sharc.config b/conf/pipeline/chipseq/sbc_sharc.config index 6fef3ba..0e66333 100644 --- a/conf/pipeline/chipseq/sbc_sharc.config +++ b/conf/pipeline/chipseq/sbc_sharc.config @@ -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' ) } } diff --git a/conf/pipeline/rnaseq/sbc_sharc.config b/conf/pipeline/rnaseq/sbc_sharc.config index 8033609..d9d9878 100644 --- a/conf/pipeline/rnaseq/sbc_sharc.config +++ b/conf/pipeline/rnaseq/sbc_sharc.config @@ -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' ) } } } diff --git a/conf/pipeline/sarek/sbc_sharc.config b/conf/pipeline/sarek/sbc_sharc.config index 4ef0534..3a7f5b9 100644 --- a/conf/pipeline/sarek/sbc_sharc.config +++ b/conf/pipeline/sarek/sbc_sharc.config @@ -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' { diff --git a/conf/sbc_sharc.config b/conf/sbc_sharc.config index 6583da7..91cf4e3 100644 --- a/conf/sbc_sharc.config +++ b/conf/sbc_sharc.config @@ -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 } +