Commit 03325266 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Output files change to gz output

parent 168c2d80
......@@ -30,7 +30,7 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
def init() {
if (reference == null) reference = config("reference")
if (dbsnp == null) dbsnp = config("dbsnp")
if (outputFile == null) outputFile = outputDir + outputName + ".vcf"
if (outputFile == null) outputFile = outputDir + outputName + ".vcf.gz"
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
......
......@@ -63,7 +63,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
//SampleWide jobs
if (mergeGvcfs && gvcfFiles.size > 0) {
val newFile = outputDir + "merged.gvcf.vcf"
val newFile = outputDir + "merged.gvcf.vcf.gz"
add(CombineGVCFs(this, gvcfFiles, newFile))
gvcfFiles = List(newFile)
}
......
......@@ -71,7 +71,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val hcGvcf = new HaplotypeCaller(this)
hcGvcf.useGvcf
hcGvcf.input_file = scriptOutput.bamFiles
hcGvcf.out = outputDir + outputName + ".gvcf.vcf"
hcGvcf.out = outputDir + outputName + ".gvcf.vcf.gz"
add(hcGvcf)
scriptOutput.gvcfFile = hcGvcf.out
......
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