From f03c70ff24062373a0bdbdb9e0fa43b7b3d2bb48 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 12 Oct 2015 15:25:28 +0200
Subject: [PATCH] Added a thread correction var
---
.../sasc/biopet/core/CommandLineResources.scala | 4 +++-
.../sasc/biopet/pipelines/mapping/Mapping.scala | 14 ++++++++++++--
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
index 300cd4cdb..0fdc946e3 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
@@ -85,9 +85,11 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
this.freeze()
}
+ var threadsCorrection = 0
+
protected def combineResources(commands: List[CommandLineResources]): Unit = {
commands.foreach(_.setResources())
- nCoresRequest = Some(commands.map(_.threads).sum)
+ nCoresRequest = Some(commands.map(_.threads).sum + threadsCorrection)
_coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum
memoryLimit = Some(_coreMemory * threads)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 2f16008f6..4d051300a 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -316,7 +316,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
bwaCommand.R = Some(getReadGroupBwa)
val sortSam = new SortSam(this)
sortSam.output = output
- add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
+ val pipe = bwaCommand | sortSam
+ pipe.isIntermediate = chunking || !skipMarkduplicates
+ pipe.threadsCorrection = -1
+ add(pipe)
output
}
@@ -334,6 +337,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val ar = addAddOrReplaceReadGroups(reorderSam.output, output)
val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
Some(gsnapCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten)
+ pipe.threadsCorrection = -1
+ zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
+ zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
add(pipe)
ar._2
}
@@ -399,7 +405,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (paired) stampyCmd.R2 = R2.get
stampyCmd.readgroup = RG
stampyCmd.sanger = true
- stampyCmd.output = this.swapExt(output.getParent, output, ".bam", ".sam")
+ stampyCmd.output = this.swapExt(output.getParentFile, output, ".bam", ".sam")
stampyCmd.isIntermediate = true
add(stampyCmd)
val sortSam = SortSam(this, stampyCmd.output, output)
@@ -421,6 +427,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
bowtie.isIntermediate = true
val ar = addAddOrReplaceReadGroups(bowtie.output, output)
val pipe = new BiopetFifoPipe(this, (Some(bowtie) :: Some(ar._1) :: Nil).flatten)
+ pipe.threadsCorrection = -1
add(pipe)
ar._2
}
@@ -433,6 +440,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val ar = addAddOrReplaceReadGroups(starCommand.outputSam, output)
val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
Some(starCommand) :: Some(ar._1) :: Nil).flatten)
+ pipe.threadsCorrection = -1
+ zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
+ zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
add(pipe)
ar._2
}
--
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