From 61926852674cc8a1e828b72b3aa13d39eb809f65 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 14:49:44 +0200
Subject: [PATCH] Change List[File] to File
---
.../main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
index 07681a738..8bdf74983 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
@@ -33,10 +33,10 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input vcf file", shortName = "input", required = true)
- var input: List[File] = Nil
+ var input: File = _
@Input(doc = "Secondary vcf file", shortName = "secondary", required = true)
- var secondaryVcf: List[File] = Nil
+ var secondaryVcf: File = _
@Output(doc = "Output vcf file", shortName = "output", required = true)
var output: File = _
@@ -56,7 +56,7 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
}
override def commandLine = super.commandLine +
- repeat("-I", input) +
+ required("-I", input) +
required("-o", output) +
required("-s", secondaryVcf) +
repeat("-f", fields.map(x => x._1 + ":" + x._2 + ":" + x._3.getOrElse("none")))
--
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