Commit c2087e09 authored by Sander Bollen's avatar Sander Bollen

put bed conversion in kopisu method

parent b220a035
......@@ -42,6 +42,11 @@
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
......
......@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage
import nl.lumc.sasc.biopet.extensions.tools.XcnvToBed
import nl.lumc.sasc.biopet.extensions.xhmm._
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -98,6 +99,17 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
genotype.outputVcf = new File(xhmmDir, "xhmm.vcf")
add(genotype)
// create bed files
val bedDir = new File(xhmmDir, "beds")
val beds = inputBams.keys.map{ x =>
val z = new XcnvToBed(this)
z.inputXcnv = discover.outputXcnv
z.sample = x
z.outpuBed = new File(bedDir, s"$x.bed")
z
}
addAll(beds)
addSummaryJobs()
}
......
Markdown is supported
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