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

process {
  withName:APPLYBQSR {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:APPLYBQSR_SPARK {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_APPLYVQSR {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_BASERECALIBRATOR {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_BASERECALIBRATOR_SPARK {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_CALCULATECONTAMINATION {  
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_CNNSCOREVARIANTS {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_CREATESEQUENCEDICTIONARY {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_ESTIMATELIBRARYCOMPLEXITY {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_FILTERMUTECTCALLS {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_FILTERVARIANTTRANCHES {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_GATHERBQSRREPORTS {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_GATHERPILEUPSUMMARIES {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_GENOMICSDBIMPORT {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_GENOTYPEGVCFS {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_GETPILEUPSUMMARIES {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_HAPLOTYPECALLER {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_INTERVALLISTTOBED {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_LEARNREADORIENTATIONMODEL {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_MARKDUPLICATES {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_MARKDUPLICATES_SPARK {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_MERGEMUTECTSTATS {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_MERGEVCFS {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_MUTECT2 {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
  withName:GATK4_VARIANTRECALIBRATOR {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
}