Commit 608c6349 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed file names

parent d0a06da2
......@@ -34,11 +34,13 @@ class Delly(val root: Configurable) extends SvCaller {
val catVariants = new CatVariants(this)
catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf")
catVariants.isIntermediate = true
if (del) {
val delly = new DellyCaller(this)
delly.input = bamFile
delly.analysistype = "DEL"
delly.isIntermediate = true
delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
add(delly)
......@@ -48,6 +50,7 @@ class Delly(val root: Configurable) extends SvCaller {
val delly = new DellyCaller(this)
delly.input = bamFile
delly.analysistype = "DUP"
delly.isIntermediate = true
delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
add(delly)
......@@ -57,6 +60,7 @@ class Delly(val root: Configurable) extends SvCaller {
val delly = new DellyCaller(this)
delly.input = bamFile
delly.analysistype = "INV"
delly.isIntermediate = true
delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
add(delly)
......@@ -66,6 +70,7 @@ class Delly(val root: Configurable) extends SvCaller {
val delly = new DellyCaller(this)
delly.input = bamFile
delly.analysistype = "TRA"
delly.isIntermediate = true
delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
add(delly)
......@@ -78,7 +83,7 @@ class Delly(val root: Configurable) extends SvCaller {
val compressedVCF = new SortVcf(this)
compressedVCF.input = catVariants.outputFile
compressedVCF.output = catVariants + ".gz"
compressedVCF.output = catVariants.outputFile + ".gz"
add(compressedVCF)
addVCF(sample, compressedVCF.output)
......
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