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Nextflow config: rework memory scaling to use resourceLimits directive #1060

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merged 3 commits into from
Aug 14, 2025
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Nextflow config: rework memory scaling to use resourceLimits directive #1060

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c2c0ed4
Nextflow config: rework memory scaling to use resourceLimits directive
DriesSchaumont Aug 13, 2025
e33e825
Add CHANGELOG entry
DriesSchaumont Aug 13, 2025
c8de368
Set last attempt to maximum memory when specified
DriesSchaumont Aug 13, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -59,6 +59,8 @@ Warning: These experimental features are subject to change in future releases.

* `workflows/multiomics/process_samples`: Add optional `--skip_scrublet_doublet_detection` flag to bypass Scrublet doublet detection. Scrublet doublet detection runs by default and can now be optionally disabled (PR #1049).

* Nextflow runner: use `resourceLimits` directive in the labels config to set a global limit on the memory (PR #1060).

## BUG FIXES

* `cellranger_multi`: Fix error when running Cell Ranger without any computational resources specified (PR #1056)
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34 changes: 8 additions & 26 deletions src/workflows/utils/labels.config
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Expand Up @@ -6,7 +6,10 @@ process {
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = null

// The memory a task is assinged increases with each attempt
// uncomment the line below and adjust the value to set a global upper limit on the memory.
// resourceLimits = [ memory: 240.Gb ]

// CPU resources
withLabel: singlecpu { cpus = 1 }
Expand All @@ -15,10 +18,10 @@ process {
withLabel: highcpu { cpus = 20 }

// Memory resources
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
withLabel: lowmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 4.GB * task.attempt } }
withLabel: midmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 25.GB * task.attempt } }
withLabel: highmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 50.GB * task.attempt } }
withLabel: veryhighmem { memory = { task?.resourceLimits?.memory && task?.maxRetries && task.attempt >= task.maxRetries ? task.resourceLimits.memory : 75.GB * task.attempt } }

// Disk space
withLabel: lowdisk {
Expand All @@ -43,24 +46,3 @@ process {
// withLabel: highdisk { disk = { 200.GB * task.attempt } }
// withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
}

def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}

try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}
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