Commit d0a06da2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Sortvcf on the end

parent 57b31904
......@@ -33,7 +33,7 @@ class Delly(val root: Configurable) extends SvCaller {
val dellyDir = new File(outputDir, sample)
val catVariants = new CatVariants(this)
catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf.gz")
catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf")
if (del) {
val delly = new DellyCaller(this)
......@@ -42,12 +42,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
add(delly)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
catVariants.variant :+= delly.outputvcf
}
if (dup) {
val delly = new DellyCaller(this)
......@@ -56,12 +51,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
add(delly)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
catVariants.variant :+= delly.outputvcf
}
if (inv) {
val delly = new DellyCaller(this)
......@@ -70,12 +60,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
add(delly)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
catVariants.variant :+= delly.outputvcf
}
if (tra) {
val delly = new DellyCaller(this)
......@@ -84,18 +69,19 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
add(delly)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
catVariants.variant :+= delly.outputvcf
}
require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly")
add(catVariants)
addVCF(sample, catVariants.outputFile)
val compressedVCF = new SortVcf(this)
compressedVCF.input = catVariants.outputFile
compressedVCF.output = catVariants + ".gz"
add(compressedVCF)
addVCF(sample, compressedVCF.output)
}
}
}
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