From 33f456b9dcb3ee0f5c7c1476596d04d5e189ada7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 28 Jan 2015 15:46:47 +0100
Subject: [PATCH] Renaming values
---
.../sasc/biopet/pipelines/basty/Basty.scala | 6 +++---
.../biopet/pipelines/gatk/GatkPipeline.scala | 6 +++---
.../sasc/biopet/core/MultiSampleQScript.scala | 18 +++++++++---------
.../MultisamplePipelineTemplate.scala | 4 ++--
.../lumc/sasc/biopet/pipelines/sage/Sage.scala | 6 +++---
5 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 4cfc75840..0f2eed5d1 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -34,14 +34,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
- protected def addLibJobsInternal(): Unit = {}
+ protected def addJobs(): Unit = {}
}
var output: FastaOutput = _
var outputSnps: FastaOutput = _
- protected def addSampleJobsInternal(): Unit = {
- runLibsJobs()
+ protected def addJobs(): Unit = {
+ addLibsJobs()
output = addGenerateFasta(sampleId, sampleDir)
outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 87f073148..8ea6f9706 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -54,7 +54,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling.sampleID = sampleId
gatkVariantcalling.outputDir = libDir
- protected def addLibJobsInternal(): Unit = {
+ protected def addJobs(): Unit = {
val bamFile: Option[File] = if (config.contains("R1")) {
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
@@ -126,8 +126,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling.sampleID = sampleId
gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
- protected def addSampleJobsInternal(): Unit = {
- runLibsJobs()
+ protected def addJobs(): Unit = {
+ addLibsJobs()
gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
gatkVariantcalling.preProcesBams = false
if (!singleSampleCalling) {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 25a464aec..7ee91c858 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -47,10 +47,10 @@ trait MultiSampleQScript extends BiopetQScript {
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
/** Adds the library jobs */
- final def addLibJobs(): Unit = {
+ final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
currentLib = Some(libraryId)
- addLibJobsInternal()
+ addJobs()
currentLib = None
currentSample = None
}
@@ -62,7 +62,7 @@ trait MultiSampleQScript extends BiopetQScript {
def libDir = sampleDir + "lib_" + libraryId + File.separator
/** Function that add library jobs */
- protected def addLibJobsInternal()
+ protected def addJobs()
}
/** Library type, need implementation in pipeline */
@@ -84,19 +84,19 @@ trait MultiSampleQScript extends BiopetQScript {
}
/** Adds sample jobs */
- final def addSampleJobs(): Unit = {
+ final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
- addSampleJobsInternal()
+ addJobs()
currentSample = None
}
/** Function to add sample jobs */
- protected def addSampleJobsInternal()
+ protected def addJobs()
/** function runs all libraries in one call */
- protected final def runLibsJobs(): Unit = {
+ protected final def addLibsJobs(): Unit = {
for ((libraryId, library) <- libraries) {
- library.addLibJobs()
+ library.addAndTrackJobs()
}
}
@@ -132,7 +132,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** Runs runSingleSampleJobs method for each sample */
final def addSamplesJobs() {
for ((sampleId, sample) <- samples) {
- sample.addSampleJobs()
+ sample.addAndTrackJobs()
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
index deb4f247e..1ccf16f42 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
@@ -27,12 +27,12 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
- protected def addLibJobsInternal(): Unit = {
+ protected def addJobs(): Unit = {
// Library jobs
}
}
- protected def addSampleJobsInternal(): Unit = {
+ protected def addJobs(): Unit = {
// Sample jobs
}
}
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 535e49424..851e8481c 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -74,7 +74,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.libraryId = libraryId
mapping.sampleId = sampleId
- protected def addLibJobsInternal(): Unit = {
+ protected def addJobs(): Unit = {
flexiprep.outputDir = libDir + "flexiprep/"
flexiprep.input_R1 = inputFastq
flexiprep.init
@@ -102,8 +102,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
}
- protected def addSampleJobsInternal(): Unit = {
- runLibsJobs()
+ protected def addJobs(): Unit = {
+ addLibsJobs()
val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
val libraryFastqFiles = libraries.map(_._2.prefixFastq).toList
--
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