Commit b3e3f3f2 authored by wyleung's avatar wyleung
Browse files

Add relative links to the results folder

parent 22991efc
......@@ -8,6 +8,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge }
import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Clever }
......@@ -96,17 +97,25 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
sampleOutput.vcf += ("clever" -> List(clever.outputvcf))
add(clever)
val clever_vcf = Ln(this, clever.outputvcf, svcallingDir + sampleID + ".clever.vcf", relative = true)
add(clever_vcf)
val breakdancerDir = svcallingDir + sampleID + ".breakdancer/"
val breakdancer = Breakdancer(this, bamFile, this.reference, breakdancerDir)
sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputvcf))
addAll(breakdancer.functions)
val bd_vcf = Ln(this, breakdancer.outputvcf, svcallingDir + sampleID + ".breakdancer.vcf", relative = true)
add(bd_vcf)
// for pindel we should use per library config collected into one config file
// val pindelDir = svcallingDir + sampleID + ".pindel/"
// val pindel = Pindel(this, bamFile, this.reference, pindelDir)
// sampleOutput.vcf += ("pindel" -> List(pindel.outputvcf))
// addAll(pindel.functions)
//
// val pindel_vcf = Ln(this, pindel.outputvcf, svcallingDir + sampleID + ".pindel.vcf", relative = true)
// add(pindel_vcf)
//
return sampleOutput
}
......
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