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eva.config
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eva.config
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// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'James A. Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/sarek EVA profile provided by nf-core/configs'
}
env {
_JAVA_OPTIONS = "-XX:ParallelGCThreads=1"
OPENBLAS_NUM_THREADS = 1
OMP_NUM_THREADS = 1
}
process {
withName:GATK4_APPLYBQSR {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_APPLYBQSR_SPARK {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_APPLYVQSR {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_BASERECALIBRATOR {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_BASERECALIBRATOR_SPARK {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_CALCULATECONTAMINATION {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_CNNSCOREVARIANTS {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_CREATESEQUENCEDICTIONARY {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_ESTIMATELIBRARYCOMPLEXITY {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_FILTERMUTECTCALLS {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_FILTERVARIANTTRANCHES {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_GATHERBQSRREPORTS {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_GATHERPILEUPSUMMARIES {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_GENOMICSDBIMPORT {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_GENOTYPEGVCFS {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_GETPILEUPSUMMARIES {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_HAPLOTYPECALLER {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_INTERVALLISTTOBED {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_LEARNREADORIENTATIONMODEL {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_MARKDUPLICATES {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_MARKDUPLICATES_SPARK {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_MERGEMUTECTSTATS {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_MERGEVCFS {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_MUTECT2 {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
withName:GATK4_VARIANTRECALIBRATOR {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
}
}