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Emphasise base.config values SHOULD be adjusted on a per-pipeline basis by developer #4360

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Emphasise base.config values SHOULD be adjusted on a per-pipeline basis by developer #4360

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7 changes: 5 additions & 2 deletions nf_core/pipeline-template/conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,7 @@ process {
// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
// If possible, it would be nice to keep the same label naming convention when
// adding in your local modules too.
// TODO nf-core: Customise requirements for specific processes.
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
// TODO nf-core: adjust all CPU, memory, and time resource requests to work with 'average' data for the pipeline

@ammaraziz ammaraziz Jun 30, 2026

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I would add stronger language:

// TODO nf-core: adjust all CPU, memory, and time resource requests to work with 'average' data for the pipeline
//        Default resource usage limits are intentionally generous and are may not be suitable. 
//        It is highly recommended to modify these settings to suit your pipeline.

@jfy133 jfy133 Jun 30, 2026

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Suggested change
// TODO nf-core: adjust all CPU, memory, and time resource requests to work with 'average' data for the pipeline
// TODO nf-core: adjust all CPU, memory, and time resource requests to work with 'average' data for the pipeline
// Default resource usage limits are intentionally generous and are may not be suitable.
// It is highly recommended to modify these settings to suit your pipeline.

withLabel:process_single {
cpus = { 1 }
memory = { 6.GB * task.attempt }
Expand Down Expand Up @@ -66,4 +65,8 @@ process {
ext.use_gpu = { workflow.profile.contains('gpu') }
accelerator = { workflow.profile.contains('gpu') ? 1 : null }
}

// TODO nf-core: If required, customise requirements for specific processes using the withName selector
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors

}
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