From d490171470edd7f15092e1f49f39a7e5b4b39dab Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Wed, 20 Jan 2016 17:30:04 +0100
Subject: [PATCH] Add pindel2vcf to pipeline
---
.../pipelines/shiva/svcallers/Pindel.scala | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index 0e0aed54f..ee4d8289b 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -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)
}
}
--
GitLab