From a2c583e8e5f1e2849d4ab8c29f5c5a3fa7131a51 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 23 Sep 2015 09:48:37 +0200
Subject: [PATCH] Reference is not used in here
---
.../biopet/pipelines/gentrap/extensions/CustomVarScan.scala | 5 +----
1 file changed, 1 insertion(+), 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 5ffce6a1c..8871f481f 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
@@ -35,9 +35,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction wi
@Input(doc = "Input BAM file", required = true)
var input: File = null
- @Input(doc = "Reference FASTA file", required = true)
- var reference: File = null
-
@Output(doc = "Output VCF file", required = true)
var output: File = null
@@ -93,7 +90,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction wi
override def beforeGraph(): Unit = {
super.beforeGraph()
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
- if (reference == null) reference = referenceFasta()
+ deps :+= referenceFasta()
}
def cmdLine: String = {
--
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