From 6b190fbd65fa64f21c9752f6afa2db0306117f62 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 21 Sep 2015 18:55:26 +0200
Subject: [PATCH] Fix reference in varscan
---
.../pipelines/gentrap/extensions/CustomVarScan.scala | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index 1ce8465ca..5ffce6a1c 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */
// FIXME: generalize piping instead of building something by hand like this!
// Better to do everything quick and dirty here rather than something half-implemented with the objects
-class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction { wrapper =>
+class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction with Reference { wrapper =>
override def configName = "customvarscan"
@@ -36,7 +36,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
var input: File = null
@Input(doc = "Reference FASTA file", required = true)
- var reference: File = config("reference")
+ var reference: File = null
@Output(doc = "Output VCF file", required = true)
var output: File = null
@@ -49,7 +49,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
this.input = List(wrapper.input)
override def configName = wrapper.configName
disableBaq = true
- reference = config("reference")
depth = Option(1000000)
outputMappingQuality = true
}
@@ -92,7 +91,9 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
}
override def beforeGraph(): Unit = {
+ super.beforeGraph()
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
+ if (reference == null) reference = referenceFasta()
}
def cmdLine: String = {
--
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