From 23084ff1e531f1da267b74a565f94e2bac28e586 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 May 2014 10:40:21 +0200
Subject: [PATCH] - output file for star
---
.../java/nl/lumc/sasc/biopet/wrappers/Star.scala | 4 ++--
.../nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 14 +++-----------
.../sasc/biopet/pipelines/mapping/Mapping.scala | 2 +-
3 files changed, 6 insertions(+), 14 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
index f898b6676..b599fae78 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
@@ -18,7 +18,7 @@ class Star(private var globalConfig: Config) extends CommandLineFunction {
@Input(doc="Fastq file R2", shortName="R2", required=false) var R2: File = _
@Argument(doc="Output Directory", shortName="outputDir") var outputDir: String = _
@Argument(doc="GenomeDir", required=false) var genomeDir: String = _
- if (genomeDir == null) genomeDir = config.getAsString("genomeDir", referenceFile.getParent + "/star")
+ if (genomeDir == null) genomeDir = config.getAsString("genomeDir", referenceFile.getParent + "/star/ref")
@Argument(doc="STAR runmode", shortName="runmode", required=false) var runmode: String = _
@@ -30,7 +30,7 @@ class Star(private var globalConfig: Config) extends CommandLineFunction {
if (threads > maxThreads) threads = maxThreads
nCoresRequest = Option(threads)
- @Output var outputSam: File = new File(outputDir + "/star_output.sam")
+ @Output var outputSam: File = new File(outputDir + "/Aligned.out.sam")
def commandLine : String= {
//init()
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 120a97a86..0b3e73391 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
@@ -91,7 +91,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
//indel recal
val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
- this.input +:= genotypeGVCFs.out
+ this.input +:= snpApplyRecalibration.out
this.nt = 4
this.memoryLimit = 2 * nt
this.recal_file = swapExt(genotypeGVCFs.out,".vcf",".indel.recal")
@@ -104,10 +104,10 @@ class Gatk(private var globalConfig: Config) extends QScript {
add(indelVariantRecalibrator)
val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments {
- this.input +:= genotypeGVCFs.out
+ this.input +:= snpApplyRecalibration.out
this.recal_file = indelVariantRecalibrator.recal_file
this.tranches_file = indelVariantRecalibrator.tranches_file
- this.out = swapExt(genotypeGVCFs.out,".vcf",".indel.recal.vcf")
+ this.out = swapExt(genotypeGVCFs.out,".recal.vcf",".indel.recal.vcf")
this.ts_filter_level = 99.0
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
this.nt = 3
@@ -115,14 +115,6 @@ class Gatk(private var globalConfig: Config) extends QScript {
if (scatterCount > 1) this.scatterCount = scatterCount
}
add(indelApplyRecalibration)
-
- // merge snp and indels
- val catVariants = new CatVariants() {
- this.variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
- this.outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
- this.reference = referenceFile
- }
- add(catVariants)
} else logger.warn("No gVCFs to genotype")
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 2e07f081b..df4d26fb6 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
@@ -88,7 +88,7 @@ class Mapping(private var globalConfig: Config) extends QScript {
bamFile = addSortSam(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
} else if (aligner == "star") {
val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/" ;
- outputSam = new File(this.outputDir + "/star_output.sam") }
+ outputSam = new File(this.outputDir + "/Aligned.out.sam") }
add(starCommand)
bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir)
}
--
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