From e5e0343443975b7314daf173490c42dd264a24ba Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 16:17:26 +0100
Subject: [PATCH] Rename afterGraph to beforeGraph
---
.../biopet/extensions/gatk/ApplyRecalibration.scala | 4 ++--
.../sasc/biopet/extensions/gatk/BaseRecalibrator.scala | 2 +-
.../sasc/biopet/extensions/gatk/HaplotypeCaller.scala | 4 ++--
.../sasc/biopet/extensions/gatk/UnifiedGenotyper.scala | 4 ++--
.../lumc/sasc/biopet/extensions/gatk/VariantEval.scala | 8 ++++----
.../biopet/core/BiopetCommandLineFunctionTrait.scala | 7 +++----
.../biopet/core/BiopetJavaCommandLineFunction.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/Raxml.scala | 4 ++--
.../nl/lumc/sasc/biopet/extensions/RunGubbins.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/extensions/Sickle.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/Star.scala | 10 +++++-----
.../scala/nl/lumc/sasc/biopet/extensions/TopHat.scala | 2 +-
.../sasc/biopet/extensions/conifer/ConiferExport.scala | 2 +-
.../biopet/extensions/igvtools/IGVToolsCount.scala | 4 ++--
.../sasc/biopet/extensions/macs2/Macs2CallPeak.scala | 2 +-
.../extensions/picard/CollectGcBiasMetrics.scala | 2 +-
.../extensions/picard/CollectInsertSizeMetrics.scala | 2 +-
.../sasc/biopet/extensions/picard/MarkDuplicates.scala | 4 ++--
.../lumc/sasc/biopet/extensions/picard/SortSam.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 4 ++--
.../lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala | 2 +-
.../sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala | 2 +-
25 files changed, 45 insertions(+), 46 deletions(-)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
index 8728b6c65..ccdce3411 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
@@ -11,8 +11,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
scatterCount = config("scattercount", default = 0)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
nt = Option(getThreads(3))
memoryLimit = Option(nt.getOrElse(1) * 2)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
index c07a2a66c..e6cc3aaf6 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
@@ -22,7 +22,7 @@ object BaseRecalibrator {
val br = new BaseRecalibrator(root)
br.input_file :+= input
br.out = output
- br.afterGraph
+ br.beforeGraph
return br
}
}
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index b8f4ea4ef..18b4f0641 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -35,8 +35,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_emit_conf = config("stand_emit_conf", default = 0)
}
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 26936df75..684c2123a 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -8,8 +8,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.core.config.Configurable
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
index c7956cab1..a9d252fde 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
@@ -9,8 +9,8 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
}
}
@@ -21,7 +21,7 @@ object VariantEval {
vareval.eval = Seq(sample)
vareval.comp = Seq(compareWith)
vareval.out = output
- vareval.afterGraph
+ vareval.beforeGraph
return vareval
}
@@ -35,7 +35,7 @@ object VariantEval {
vareval.ST = ST
vareval.noEV = true
vareval.EV = EV
- vareval.afterGraph
+ vareval.beforeGraph
return vareval
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 905b3a715..f0c2f37c6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -51,15 +51,14 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
* Can overr
* ide this method. This is executed after the script is done en queue starts to generate the graph
*/
- protected[core] def afterGraph {}
- //TODO: function need rename to beforeGraph
+ protected[core] def beforeGraph {}
/**
* Set default output file, threads and vmem for current job
*/
override def freezeFieldValues() {
checkExecutable
- afterGraph
+ beforeGraph
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads)
@@ -126,7 +125,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
addJobReportBinding("cores", nCoresRequest match {
case Some(n) if n > 0 => n
- case _ => 1
+ case _ => 1
})
addJobReportBinding("version", getVersion)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 8f479ae97..b0657e369 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -37,8 +37,8 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
/**
* Sets memory limit
*/
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
memoryLimit = config("memory_limit")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 8b6b0a6f5..807555d60 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -72,7 +72,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
for (function <- functions) function match {
case f: BiopetCommandLineFunctionTrait => {
f.checkExecutable
- f.afterGraph
+ f.beforeGraph
f.commandLine
}
case _ =>
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 7bda87925..8edf474e7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -48,7 +48,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
override val defaultThreads = 4
- override def afterGraph {
+ override def beforeGraph {
this.checkExecutable
val fastqcDir = new File(executable).getParent
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index 1d7b45ec9..991325495 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -64,10 +64,10 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var executableNonThreads: String = config("exe", default = "raxmlHPC")
var executableThreads: Option[String] = config("exe_pthreads")
- override def afterGraph {
+ override def beforeGraph {
if (threads == 0) threads = getThreads(defaultThreads)
executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
- super.afterGraph
+ super.beforeGraph
out +:= getInfoFile
f match {
case "d" if b.isEmpty => {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index e732c1023..a041f5dc7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -47,8 +47,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var verbose: Boolean = config("verbose", default = false)
var noCleanup: Boolean = config("no_cleanup", default = false)
- override def afterGraph: Unit = {
- super.afterGraph
+ override def beforeGraph: Unit = {
+ super.beforeGraph
jobLocalDir = new File(outputDirectory)
if (prefix.isEmpty) prefix = Some(fastafile.getName)
val out: List[String] = List(".recombination_predictions.embl",
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index 5056c70ab..abc517962 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -53,7 +53,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
override val versionRegex = """sickle version (.*)""".r
override def versionCommand = executable + " --version"
- override def afterGraph {
+ override def beforeGraph {
if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index f8e337649..42a290825 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -62,7 +62,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultVmem = "6G"
override val defaultThreads = 8
- override def afterGraph() {
+ override def beforeGraph() {
if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
if (runmode == null) {
@@ -103,7 +103,7 @@ object Star {
star.outputDir = outputDir
star.isIntermediate = isIntermediate
star.deps = deps
- star.afterGraph
+ star.beforeGraph
return star
}
@@ -111,20 +111,20 @@ object Star {
val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass1"))
starCommand_pass1.isIntermediate = isIntermediate
starCommand_pass1.deps = deps
- starCommand_pass1.afterGraph
+ starCommand_pass1.beforeGraph
val starCommand_reindex = new Star(configurable)
starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
starCommand_reindex.outputDir = new File(outputDir, "re-index")
starCommand_reindex.runmode = "genomeGenerate"
starCommand_reindex.isIntermediate = isIntermediate
- starCommand_reindex.afterGraph
+ starCommand_reindex.beforeGraph
val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass2"))
starCommand_pass2.genomeDir = starCommand_reindex.outputDir
starCommand_pass2.isIntermediate = isIntermediate
starCommand_pass2.deps = deps
- starCommand_pass2.afterGraph
+ starCommand_pass2.beforeGraph
return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
index 98ee6de52..ce86a1ed9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
@@ -64,7 +64,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --version"
- override def afterGraph() {
+ override def beforeGraph() {
if (!outputDir.endsWith("/")) outputDir += "/"
output = new File(outputDir + "accepted_hits.bam")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
index 02c0f0958..c7b816953 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
@@ -28,7 +28,7 @@ class ConiferExport(val root: Configurable) extends Conifer {
@Output(doc = "Output <sample>.svdzrpkm.bed", shortName = "out", required = true)
var output: File = _
- override def afterGraph {
+ override def beforeGraph {
this.checkExecutable
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index 803761683..d3f4e6ccc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -44,8 +44,8 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index e6a9c48e9..8224fd471 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -55,7 +55,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var broadcutoff: Option[Int] = config("broadcutoff")
var callsummits: Boolean = config("callsummits", default = false)
- override def afterGraph: Unit = {
+ override def beforeGraph: Unit = {
if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
output_narrow = new File(outputdir + name.get + ".narrowPeak")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 8d1b2c45e..86198d2a3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -49,7 +49,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
@Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
var isBisulfiteSequinced: Option[Boolean] = config("isbisulfitesequinced")
- override def afterGraph {
+ override def beforeGraph {
if (outputChart == null) outputChart = new File(output + ".pdf")
//require(reference.exists)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 77ceb0e58..9b1777677 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -54,7 +54,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
@Argument(doc = "HISTOGRAM_WIDTH", required = false)
var histogramWidth: Option[Int] = config("histogramWidth")
- override def afterGraph {
+ override def beforeGraph {
if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
//require(reference.exists)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 6df04c12c..181494ae1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -70,8 +70,8 @@ class MarkDuplicates(val root: Configurable) extends Picard {
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 56cfec1dd..ef7ec250d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -34,8 +34,8 @@ class SortSam(val root: Configurable) extends Picard {
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index c431aa0da..3eec803c8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -49,8 +49,8 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
override val defaultVmem = "8G"
memoryLimit = Option(4)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index ae21c34e4..3e9743fb1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -54,8 +54,8 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
override def defaults = ConfigUtils.mergeMaps(Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1)),
super.defaults)
- override def afterGraph {
- super.afterGraph
+ override def beforeGraph {
+ super.beforeGraph
val samtoolsMpileup = new SamtoolsMpileup(this)
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index bf63f0415..1bd5b1df7 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -173,7 +173,7 @@ object Fastqc {
if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
fastqcCommand.output = new File(outDir, "/" + filename + "_fastqc.zip")
- fastqcCommand.afterGraph
+ fastqcCommand.beforeGraph
fastqcCommand
}
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index 05236e13c..03144feee 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -38,7 +38,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
}
}
- override def afterGraph {
+ override def beforeGraph {
if (fastqc != null) deps ::= fastqc.output
}
--
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