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74 lines
2.3 KiB
Text
74 lines
2.3 KiB
Text
/*
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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/chipseq
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// process-specific resource requirements - reduced specification from those in chipseq/conf/base.config
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process {
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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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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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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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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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}
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// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min(obj, params.max_cpus as int)
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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}
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}
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}
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