F72.config

process {
    withName: run_validate_PipeVal {
        cpus = 1
        memory = 1.GB
    }
    withName: extract_GenomeIntervals {
        cpus = 1
        memory = 1.GB
    }
    withName: run_SplitIntervals_GATK {
        cpus = 1
        memory = 1.GB
    }
    withName: run_RealignerTargetCreator_GATK {
        cpus = 6
        memory = 10.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: run_IndelRealigner_GATK {
        cpus = 6
        memory = 10.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 4
            }
        }
    }
    withName: run_BaseRecalibrator_GATK {
        cpus = 1
        memory = 72.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: run_ApplyBQSR_GATK {
        cpus = 1
        memory = 2.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 4
            }
        }
    }
    withName: run_MergeSamFiles_Picard {
        cpus = 2
        memory = 8.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: deduplicate_records_SAMtools {
        cpus = 2
        memory = 8.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: run_index_SAMtools {
        cpus = 1
        memory = 2.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: run_GetPileupSummaries_GATK {
        cpus = 1
        memory = 5.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: run_CalculateContamination_GATK {
        cpus = 1
        memory = 5.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: run_DepthOfCoverage_GATK {
        cpus = 1
        memory = 10.GB
        retry_strategy {
            memory {
                strategy = 'exponential'
                operand = 2
            }
        }
    }
    withName: remove_intermediate_files {
        cpus = 1
        memory = 1.GB
    }
    withName: remove_unmerged_BAMs {
        cpus = 1
        memory = 1.GB
    }
    withName: remove_merged_BAM {
        cpus = 1
        memory = 1.GB
    }
}