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nf-configs/conf/pipeline/sarek/eddie.config

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process {
withName:MapReads {
cpus = 16
memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
}
withName:BuildDict {
cpus = 1
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:BamQC {
cpus = 8
memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
}
withName:MarkDuplicates {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:BaseRecalibrator {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:ApplyBQSR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GatherBQSRReports {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:HaplotypeCaller {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GenotypeGVCFs {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:Mutect2 {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:MergeMutect2Stats {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:PileupSummariesForMutect2 {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:MergePileupSummaries {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:CalculateContamination {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:FilterMutect2Calls {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
}