Commit adb6ffe1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed own vmem

parent f42be845
......@@ -97,10 +97,11 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if (jobOutputFile == null && firstOutput != null)
jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads) + pipesJobs.map(_.threads).map(i => if (i == 0) 1 else i).sum
val ownThreads = getThreads(defaultThreads)
if (threads == 0) threads = ownThreads + pipesJobs.map(_.threads).map(i => if (i == 0) 1 else i).sum
if (threads > 1) nCoresRequest = Option(threads)
_coreMemory = config("core_memory", default = defaultCoreMemory +
_coreMemory = config("core_memory", default = (defaultCoreMemory * (ownThreads.toDouble / this.threads.toDouble)) +
pipesJobs.map(job => job.coreMemeory * (job.threads.toDouble / this.threads.toDouble)).sum).asDouble +
(0.5 * retry)
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import nl.lumc.sasc.biopet.core.summary.{SummaryQScript, Summarizable}
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetPipe }
import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
......@@ -43,11 +43,11 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
clip match {
case Some(job) => qscript.addSummarizable(job, s"clipping_$read")
case _ =>
case _ =>
}
trim match {
case Some(job) => qscript.addSummarizable(job, s"trimming_$read")
case _ =>
case _ =>
}
}
......
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