Commit d4901714 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Add pindel2vcf to pipeline

parent 2e9fffdb
......@@ -16,11 +16,12 @@
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import java.io.File
import java.text.SimpleDateFormat
import java.util.Calendar
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelCaller$, PindelConfig }
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.extensions.pindel._
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/// Pindel is actually a mini pipeline executing binaries from the pindel package
class Pindel(val root: Configurable) extends SvCaller {
......@@ -32,7 +33,7 @@ class Pindel(val root: Configurable) extends SvCaller {
for ((sample, bamFile) <- inputBams) {
val pindelDir = new File(outputDir, sample)
val config_file: File = new File(outputDir + "." + sample + ".pindel.cfg")
val config_file: File = new File(pindelDir, sample + ".pindel.cfg")
val cfg = new PindelConfig(this)
cfg.input = bamFile
......@@ -44,6 +45,16 @@ class Pindel(val root: Configurable) extends SvCaller {
val pindel = PindelCaller(this, cfg.output, pindelDir)
add(pindel)
// Current date
val today = Calendar.getInstance().getTime()
val todayformat = new SimpleDateFormat("yyyyMMdd")
val pindelVcf = new PindelVCF(this)
pindelVcf.pindelOutputRoot = Some(pindelDir)
pindelVcf.referenceDate = todayformat.format(today) // officially, we should enter the date of the genome here
pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
add(pindelVcf)
}
}
......
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