c00bcda3f8
Build pipeline: viash-hub.rnaseq.main-k4ttq
Source commit: f52978a0e2
Source message: Fix summarizedexperiment build (#42)
45 lines
1.5 KiB
Plaintext
45 lines
1.5 KiB
Plaintext
process {
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// Default resources for components that hardly do any processing
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memory = { 2.GB * task.attempt }
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cpus = 1
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// Retry for exit codes that have something to do with memory issues
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errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
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maxRetries = 3
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maxMemory = null
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// Resource labels
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withLabel: singlecpu { cpus = 1 }
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withLabel: lowcpu { cpus = 2 }
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withLabel: midcpu { cpus = 4 }
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withLabel: highcpu { cpus = 8 }
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withLabel: veryhighcpu { cpus = 16 }
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withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
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withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
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withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
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withLabel: veryhighmem { memory = { get_memory( 48.GB * task.attempt ) } }
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}
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def get_memory(to_compare) {
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if (!process.containsKey("maxMemory") || !process.maxMemory) {
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return to_compare
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}
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try {
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if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
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return process.maxMemory
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}
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else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
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return max_memory as nextflow.util.MemoryUnit
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}
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else {
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return to_compare
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}
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} catch (all) {
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println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
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System.exit(1)
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}
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}
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