Commit 52a36f28 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix threads / memlimit

parent 2afb277b
......@@ -41,7 +41,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
nct = Some(threads)
nct = Some(getThreads(1))
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
......
......@@ -15,7 +15,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
nct = config("threads", default = 1)
nct = Some(getThreads(1))
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
......
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