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Updated process names to Sarek 3

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ameynert 2022-09-07 16:00:52 +01:00 committed by GitHub
parent d84754d328
commit 29a0b30d85
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1 changed files with 15 additions and 15 deletions
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conf/pipeline/sarek/eddie.config
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@ -1,53 +1,53 @@
process { process {
withName:MapReads { withName:BWAMEM_MEM {
cpus = 16 cpus = 16
memory = 128.GB memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
} }
withName:BuildDict { withName:GATK4_CREATESEQUENCEDICTIONARY {
cpus = 1 cpus = 1
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:BamQC { withName:QUALIMAP_BAMQC {
cpus = 8 cpus = 8
memory = 128.GB memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
} }
withName:MarkDuplicates { withName:GATK4_MARKDUPLICATES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:BaseRecalibrator { withName:BASERECALIBRATOR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:ApplyBQSR { withName:APPLYBQSR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GatherBQSRReports { withName:GATHERBQSRREPORTS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:HaplotypeCaller { withName:GATK4_HAPLOTYPECALLER {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GenotypeGVCFs { withName:GATK4_GENOTYPEGVCFS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:Mutect2 { withName:MUTECT2 {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:MergeMutect2Stats { withName:MERGEMUTECTSTATS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:PileupSummariesForMutect2 { withName:GETPILEUPSUMMARIES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:MergePileupSummaries { withName:GATHERPILEUPSUMMARIES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:CalculateContamination { withName:CALCULATECONTAMINATION {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:FilterMutect2Calls { withName:FILTERMUTECTCALLS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
} }