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42 lines
1.5 KiB
Text
42 lines
1.5 KiB
Text
// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'Friederike Hanssen (@FriederikeHanssen)'
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config_profile_description = 'nf-core/sarek CFC profile provided by nf-core/configs'
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}
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// Specific nf-core/sarek process configuration
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process {
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withName:'StrelkaSingle|Strelka|StrelkaBP|MantaSingle|Manta' {
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cpus = { check_resource( 20 * task.attempt) }
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memory = { check_resource( 59.GB * task.attempt) }
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}
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withName:'MSIsensor_scan|MSIsensor_msi' {
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memory = { check_resource( 55.GB * task.attempt ) }
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}
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withName:BamQC {
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memory = { check_resource( 372.GB * task.attempt) }
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}
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withName:MapReads{
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cpus = { check_resource( 20 * task.attempt ) }
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memory = { check_resource( 59.GB * task.attempt) }
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}
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}
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def check_resource(obj) {
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try {
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if (obj.getClass() == nextflow.util.MemoryUnit && 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 if (obj.getClass() == nextflow.util.Duration && 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 if (obj.getClass() == java.lang.Integer)
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return Math.min(obj, params.max_cpus as int)
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}' is not valid! Using default value: $obj"
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}
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}
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