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 { ...@@ -33,7 +33,7 @@ class Delly(val root: Configurable) extends SvCaller {
val dellyDir = new File(outputDir, sample) val dellyDir = new File(outputDir, sample)
val catVariants = new CatVariants(this) val catVariants = new CatVariants(this)
catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf.gz") catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf")
if (del) { if (del) {
val delly = new DellyCaller(this) val delly = new DellyCaller(this)
...@@ -42,12 +42,7 @@ class Delly(val root: Configurable) extends SvCaller { ...@@ -42,12 +42,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf") delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
add(delly) add(delly)
val compressedVCF = new SortVcf(this) catVariants.variant :+= delly.outputvcf
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
} }
if (dup) { if (dup) {
val delly = new DellyCaller(this) val delly = new DellyCaller(this)
...@@ -56,12 +51,7 @@ class Delly(val root: Configurable) extends SvCaller { ...@@ -56,12 +51,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf") delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
add(delly) add(delly)
val compressedVCF = new SortVcf(this) catVariants.variant :+= delly.outputvcf
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
} }
if (inv) { if (inv) {
val delly = new DellyCaller(this) val delly = new DellyCaller(this)
...@@ -70,12 +60,7 @@ class Delly(val root: Configurable) extends SvCaller { ...@@ -70,12 +60,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf") delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
add(delly) add(delly)
val compressedVCF = new SortVcf(this) catVariants.variant :+= delly.outputvcf
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
} }
if (tra) { if (tra) {
val delly = new DellyCaller(this) val delly = new DellyCaller(this)
...@@ -84,18 +69,19 @@ class Delly(val root: Configurable) extends SvCaller { ...@@ -84,18 +69,19 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf") delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
add(delly) add(delly)
val compressedVCF = new SortVcf(this) catVariants.variant :+= delly.outputvcf
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compressedVCF.output
} }
require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly") require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly")
add(catVariants) 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)
} }
} }
} }
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment