From ad4b957a68f4a81efbd650aefa11b3fed8838e5a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 27 Oct 2015 14:01:33 +0100
Subject: [PATCH] Added more settings to the summary
---
.../biopet/pipelines/basty/BastyTrait.scala | 2 +-
.../biopet/pipelines/shiva/ShivaTrait.scala | 23 +++++++++++++++----
2 files changed, 19 insertions(+), 6 deletions(-)
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
index d9085369f..7da7f9c3c 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+++ b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
@@ -180,7 +180,7 @@ trait BastyTrait extends MultiSampleQScript {
snpsOnly: Boolean = false): FastaOutput = {
val bastyGenerateFasta = new BastyGenerateFasta(this)
bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
- bastyGenerateFasta.inputVcf = shiva.variantCalling.get.finalFile
+ bastyGenerateFasta.inputVcf = shiva.multisampleVariantCalling.get.finalFile
if (shiva.samples.contains(sampleName)) {
bastyGenerateFasta.bamFile = shiva.samples(sampleName).preProcessBam.get
}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index a396bb2e1..8a0cdb439 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -84,6 +84,9 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
/** Method to make a library */
def makeLibrary(id: String) = new Library(id)
+ /** Sample specific settings */
+ override def summarySettings = Map("single_sample_variantcalling" -> variantcalling.isDefined)
+
/** Class to generate jobs for a library */
class Library(libId: String) extends AbstractLibrary(libId) {
/** Library specific files to add to the summary */
@@ -101,6 +104,9 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
/** Method to execute library preprocess */
def preProcess(input: File): Option[File] = None
+ /** Library specific settings */
+ override def summarySettings = Map("library_variantcalling" -> variantcalling.isDefined)
+
/** Method to make the mapping submodule */
def makeMapping = {
val mapping = new Mapping(qscript)
@@ -280,7 +286,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
}
}
- lazy val variantCalling = if (config("multisample_variantcalling", default = true).asBoolean) {
+ lazy val multisampleVariantCalling = if (config("multisample_variantcalling", default = true).asBoolean) {
Some(makeVariantcalling(multisample = true))
} else None
@@ -288,9 +294,14 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
Some(new ShivaSvCalling(this))
} else None
+ lazy val annotation = if (multisampleVariantCalling.isDefined &&
+ config("annotation", default = false).asBoolean) {
+ Some(new Toucan(this))
+ } else None
+
/** This will add the mutisample variantcalling */
def addMultiSampleJobs(): Unit = {
- variantCalling.foreach(vc => {
+ multisampleVariantCalling.foreach(vc => {
vc.outputDir = new File(outputDir, "variantcalling")
vc.inputBams = samples.flatMap(_._2.preProcessBam).toList
vc.init()
@@ -298,8 +309,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
addAll(vc.functions)
addSummaryQScript(vc)
- if (config("annotation", default = false).asBoolean) {
- val toucan = new Toucan(this)
+ annotation.foreach { toucan =>
toucan.outputDir = new File(outputDir, "annotation")
toucan.inputVCF = vc.finalFile
toucan.init()
@@ -330,7 +340,10 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
Map(
"reference" -> referenceSummary,
"regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
- "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
+ "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed")),
+ "annotation" -> annotation.isDefined,
+ "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
+ "sv_calling" -> svCalling.isDefined
)
}
--
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