From da6a6ef23f047ad36c3503296d7939707965a017 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 May 2014 14:29:02 +0200
Subject: [PATCH] - output file for star
---
.../nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 13 +++++++------
.../sasc/biopet/pipelines/mapping/Mapping.scala | 12 ++++++------
2 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index 0b3e73391..d410395f8 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -11,6 +11,7 @@ import scala.util.parsing.json._
import org.broadinstitute.sting.utils.variant._
class Gatk(private var globalConfig: Config) extends QScript {
+ qscript =>
@Argument(doc="Config Json file",shortName="config") var configfiles: List[File] = Nil
@Argument(doc="Only Sample",shortName="sample", required=false) var onlySample: String = _
@Argument(doc="Output directory", shortName="outputDir", required=true) var outputDir: String = _
@@ -54,8 +55,8 @@ class Gatk(private var globalConfig: Config) extends QScript {
//SampleWide jobs
if (gvcfFiles.size > 0) {
val genotypeGVCFs = new GenotypeGVCFs() with gatkArguments {
- this.variant = gvcfFiles
- this.scatterCount = scatterCount
+ this.variant = qscript.gvcfFiles
+ this.scatterCount = qscript.scatterCount
this.out = new File(outputDir,"final.vcf")
}
add(genotypeGVCFs)
@@ -85,7 +86,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
this.nt = 3
this.memoryLimit = 2 * nt
- if (scatterCount > 1) this.scatterCount = scatterCount
+ if (scatterCount > 1) this.scatterCount = qscript.scatterCount
}
add(snpApplyRecalibration)
@@ -112,7 +113,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
this.nt = 3
this.memoryLimit = 2 * nt
- if (scatterCount > 1) this.scatterCount = scatterCount
+ if (scatterCount > 1) this.scatterCount = qscript.scatterCount
}
add(indelApplyRecalibration)
} else logger.warn("No gVCFs to genotype")
@@ -141,7 +142,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
// Variant calling
val haplotypeCaller = new HaplotypeCaller with gatkArguments
- if (scatterCount > 1) haplotypeCaller.scatterCount = scatterCount * 15
+ if (scatterCount > 1) haplotypeCaller.scatterCount = qscript.scatterCount * 15
haplotypeCaller.input_file = outputFiles("FinalBams")
haplotypeCaller.out = new File(outputDir,sampleID + "/" + sampleID + ".gvcf.vcf")
if (dbsnp != null) haplotypeCaller.dbsnp = dbsnp
@@ -191,7 +192,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
val bwaCommand = new Bwa(config)
bwaCommand.R1 = flexiprep.outputFiles("output_R1")
if (paired) bwaCommand.R2 = flexiprep.outputFiles("output_R2")
- bwaCommand.referenceFile = referenceFile
+ bwaCommand.referenceFile = qscript.referenceFile
bwaCommand.nCoresRequest = 8
bwaCommand.jobResourceRequests :+= "h_vmem=6G"
bwaCommand.RG = "@RG\\t" +
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index df4d26fb6..3825a8736 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -98,12 +98,12 @@ class Mapping(private var globalConfig: Config) extends QScript {
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
val sortSam = new SortSam {
- input = inputSam
- createIndex = true
- output = outputFile
- memoryLimit = 2
- nCoresRequest = 2
- jobResourceRequests :+= "h_vmem=4G"
+ this.input = inputSam
+ this.createIndex = true
+ this.output = outputFile
+ this.memoryLimit = 2
+ this.nCoresRequest = 2
+ this.jobResourceRequests :+= "h_vmem=4G"
}
add(sortSam)
--
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