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Commit adb6ffe1 authored by Peter van 't Hof's avatar Peter van 't Hof
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Changed own vmem

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