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Updated process names to Sarek 3
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parent
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1 changed files with 15 additions and 15 deletions
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@ -1,53 +1,53 @@
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process {
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withName:MapReads {
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withName:BWAMEM_MEM {
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cpus = 16
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memory = 128.GB
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clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
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}
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withName:BuildDict {
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withName:GATK4_CREATESEQUENCEDICTIONARY {
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cpus = 1
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:BamQC {
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withName:QUALIMAP_BAMQC {
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cpus = 8
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memory = 128.GB
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clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
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}
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withName:MarkDuplicates {
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withName:GATK4_MARKDUPLICATES {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:BaseRecalibrator {
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withName:BASERECALIBRATOR {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:ApplyBQSR {
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withName:APPLYBQSR {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:GatherBQSRReports {
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withName:GATHERBQSRREPORTS {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:HaplotypeCaller {
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withName:GATK4_HAPLOTYPECALLER {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:GenotypeGVCFs {
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withName:GATK4_GENOTYPEGVCFS {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:Mutect2 {
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withName:MUTECT2 {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:MergeMutect2Stats {
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withName:MERGEMUTECTSTATS {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:PileupSummariesForMutect2 {
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withName:GETPILEUPSUMMARIES {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:MergePileupSummaries {
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withName:GATHERPILEUPSUMMARIES {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:CalculateContamination {
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withName:CALCULATECONTAMINATION {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:FilterMutect2Calls {
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withName:FILTERMUTECTCALLS {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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}
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