Commit ef811002 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

fix typo

parent c1e610af
......@@ -35,13 +35,13 @@ class Breakdancer(val root: Configurable) extends SvCaller {
val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
sample = sample + "_bd")
val compresssedVCF = new SortVcf(this)
compresssedVCF.input = bdvcf.output
compresssedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
val compressedVCF = new SortVcf(this)
compressedVCF.input = bdvcf.output
compressedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
add(bdcfg, breakdancer, bdvcf, compresssedVCF)
add(bdcfg, breakdancer, bdvcf, compressedVCF)
addVCF(sample, compresssedVCF.output)
addVCF(sample, compressedVCF.output)
}
}
}
......@@ -37,12 +37,12 @@ class Clever(val root: Configurable) extends SvCaller {
cleverVCF.isIntermediate = true
add(cleverVCF)
val sortvcf = new SortVcf(this)
sortvcf.input = cleverVCF.output
sortvcf.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
add(sortvcf)
val compressedVCF = new SortVcf(this)
compressedVCF.input = cleverVCF.output
compressedVCF.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
add(compressedVCF)
addVCF(sample, sortvcf.output)
addVCF(sample, compressedVCF.output)
}
}
}
......@@ -43,12 +43,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
add(delly)
val compresssedVCF = new SortVcf(this)
compresssedVCF.input = delly.outputvcf
compresssedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
add(compresssedVCF)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compresssedVCF.output
catVariants.variant :+= compressedVCF.output
}
if (dup) {
val delly = new DellyCaller(this)
......@@ -57,12 +57,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
add(delly)
val compresssedVCF = new SortVcf(this)
compresssedVCF.input = delly.outputvcf
compresssedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
add(compresssedVCF)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compresssedVCF.output
catVariants.variant :+= compressedVCF.output
}
if (inv) {
val delly = new DellyCaller(this)
......@@ -71,12 +71,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
add(delly)
val compresssedVCF = new SortVcf(this)
compresssedVCF.input = delly.outputvcf
compresssedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
add(compresssedVCF)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compresssedVCF.output
catVariants.variant :+= compressedVCF.output
}
if (tra) {
val delly = new DellyCaller(this)
......@@ -85,12 +85,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
add(delly)
val compresssedVCF = new SortVcf(this)
compresssedVCF.input = delly.outputvcf
compresssedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
add(compresssedVCF)
val compressedVCF = new SortVcf(this)
compressedVCF.input = delly.outputvcf
compressedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
add(compressedVCF)
catVariants.variant :+= compresssedVCF.output
catVariants.variant :+= compressedVCF.output
}
require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly")
......
......@@ -59,12 +59,12 @@ class Pindel(val root: Configurable) extends SvCaller {
pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
add(pindelVcf)
val compresssedVCF = new SortVcf(this)
compresssedVCF.input = pindelVcf.outputVCF
compresssedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
add(compresssedVCF)
val compressedVCF = new SortVcf(this)
compressedVCF.input = pindelVcf.outputVCF
compressedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
add(compressedVCF)
addVCF(sample, compresssedVCF.output)
addVCF(sample, compressedVCF.output)
}
}
......
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