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@ -1,38 +1,33 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Sheffield Bioinformatics Core Configuration Profile - ShARC
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Custom Pipeline Resource Config for nf-core/sarek
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// Sheffield Bioinformatics Core Configuration Profile - ShARC
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// Custom Pipeline Resource Config for nf-core/sarek
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// process-specific resource requirements - reduced specification from those in sarek/conf/base.config
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process {
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// error and retry handling
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' }
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maxRetries = 2
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// process labels
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 6 * task.attempt, 'cpus' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 192.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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@ -41,7 +36,7 @@ process {
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}
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withLabel:process_high_memory {
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memory = { check_max( 60.GB * task.attempt, 'memory' ) }
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memory = { check_max( 240.GB * task.attempt, 'memory' ) }
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}
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@ -49,7 +44,7 @@ process {
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withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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memory = { check_max( 192.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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@ -66,11 +61,13 @@ process {
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}
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withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' {
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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}
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withName:'GATK4_MARKDUPLICATES' {
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 240.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {
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