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112 lines
3.5 KiB
Plaintext
112 lines
3.5 KiB
Plaintext
// 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( 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( 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( 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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withLabel:process_long {
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withLabel:process_high_memory {
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memory = { check_max( 240.GB * task.attempt, 'memory' ) }
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}
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// process name
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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( 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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withName:'FASTP' {
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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}
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withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT' {
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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}
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withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS' {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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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( 72.GB * task.attempt, 'memory' ) }
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}
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withName:'GATK4_MARKDUPLICATES' {
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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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cpus = { check_max( 1 * task.attempt, 'cpus' ) }
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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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