Commit 64d1f13a authored by wyleung's avatar wyleung
Browse files

Renames

parent 3f65618b
......@@ -194,17 +194,17 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
val bdcfg = BreakdancerConfig(this, input, this.configfile)
bdcfg.deps = this.deps
outputFiles += ("breakdancer_cfg" -> bdcfg.output )
outputFiles += ("cfg" -> bdcfg.output )
add( bdcfg )
val output_tsv: File = this.outputraw
val breakdancer = BreakdancerCaller( this, bdcfg.output, output_tsv )
add( breakdancer )
outputFiles += ("breakdancer_tsv" -> breakdancer.output )
outputFiles += ("tsv" -> breakdancer.output )
val bdvcf = BreakdancerVCF( this, breakdancer.output, this.outputvcf )
add( bdvcf )
outputFiles += ("breakdancer_vcf" -> bdvcf.output )
outputFiles += ("vcf" -> bdvcf.output )
}
}
......
......@@ -101,7 +101,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val breakdancerDir = svcallingDir + sampleID + ".breakdancer/"
val breakdancer = Breakdancer(this, bamFile, this.reference, breakdancerDir)
sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputraw))
sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputvcf))
addAll(breakdancer.functions)
// for pindel we should use per library config collected into one config file
......
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