From 5f8a8375d905949ac74c304c7aa3c387e3329030 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 11:51:58 +0100
Subject: [PATCH] Implemented addMultisampleJobs method
---
.../nl/lumc/sasc/biopet/pipelines/basty/Basty.scala | 9 ++++++---
.../lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala | 9 +++++----
.../biopet/pipelines/MultisamplePipelineTemplate.scala | 3 +++
.../scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 6 ++++--
.../scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala | 7 +++++--
5 files changed, 23 insertions(+), 11 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 0f2eed5d1..6ee6e73f6 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
@@ -41,7 +41,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
var outputSnps: FastaOutput = _
protected def addJobs(): Unit = {
- addLibsJobs()
+ addPerLibJobs()
output = addGenerateFasta(sampleId, sampleDir)
outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
}
@@ -56,11 +56,13 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline.biopetScript
addAll(gatkPipeline.functions)
+ addPerSampleJobs()
+ }
+
+ def addMultiSampleJobs(): Unit = {
val refVariants = addGenerateFasta(null, outputDir + "reference/", outputName = "reference")
val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", outputName = "reference", snpsOnly = true)
- addSamplesJobs()
-
val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
add(catVariants)
val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
@@ -129,6 +131,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
addTreeJobs(catVariantsSnps.output, catConsensusVariantsSnps.output, outputDir + "trees" + File.separator + "snps_only", "snps_only")
addTreeJobs(catVariants.output, catConsensusVariants.output, outputDir + "trees" + File.separator + "snps_indels", "snps_indels")
+
}
def addGenerateFasta(sampleName: String, outputDir: String, outputName: String = null,
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 8ea6f9706..c9b18c1be 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
@@ -127,7 +127,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
protected def addJobs(): Unit = {
- addLibsJobs()
+ addPerLibJobs()
gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
gatkVariantcalling.preProcesBams = false
if (!singleSampleCalling) {
@@ -150,10 +150,11 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
}
- def biopetScript() {
- addSamplesJobs
+ def biopetScript(): Unit = {
+ addPerSampleJobs
+ }
- //SampleWide jobs
+ def addMultiSampleJobs(): Unit = {
val gvcfFiles: List[File] = if (mergeGvcfs && externalGvcfs.size + samples.size > 1) {
val newFile = outputDir + "merged.gvcf.vcf.gz"
add(CombineGVCFs(this, externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile), newFile))
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 1ccf16f42..271c06085 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
@@ -37,6 +37,9 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
}
}
+ def addMultiSampleJobs(): Unit = {
+ }
+
def init(): Unit = {
}
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index cd883186a..26b070704 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -67,7 +67,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
val controls: List[String] = config("control", default = Nil)
def addJobs(): Unit = {
- addLibsJobs()
+ addPerLibJobs()
val bamFiles = libraries.map(_._2.mapping.finalBamFile).toList
if (bamFiles.length == 1) {
add(Ln(qscript, bamFiles.head, bamFile))
@@ -102,8 +102,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
// Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
logger.info("Starting CArP pipeline")
- addSamplesJobs
+ addPerSampleJobs
+ }
+ def addMultiSampleJobs(): Unit = {
for ((sampleId, sample) <- samples) {
for (controlId <- sample.controls) {
if (!samples.contains(controlId))
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 851e8481c..6c65e21bd 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
@@ -103,7 +103,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
protected def addJobs(): Unit = {
- addLibsJobs()
+ addPerLibJobs()
val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
val libraryFastqFiles = libraries.map(_._2.prefixFastq).toList
@@ -151,7 +151,10 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
tagsLibrary = cdl.output
}
- addSamplesJobs
+ addPerSampleJobs
+ }
+
+ def addMultiSampleJobs(): Unit = {
}
def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: String) {
--
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