From d70e89308265b8fc423878314d496f04c3f62ab1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 21:13:52 +0100
Subject: [PATCH] Fix some config values
---
.../scala/nl/lumc/sasc/biopet/extensions/Stampy.scala | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index 1db8f6d67..bb412a8fb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -54,9 +54,9 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var sensitive: Boolean = config("sensitive", default = false)
var fast: Boolean = config("fast", default = false)
- var readgroup: String = config("readgroup")
+ var readgroup: String = null
var verbosity: Option[Int] = config("verbosity", default = 2)
- var logfile: String = config("logfile")
+ var logfile: Option[String] = config("logfile")
executable = config("exe", default = "stampy.py", freeVar = false)
override val versionRegex = """stampy v(.*) \(.*\), .*""".r
@@ -68,6 +68,11 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --help"
+ override def beforeGraph: Unit = {
+ super.beforeGraph
+ require(readgroup != null)
+ }
+
def cmdLine: String = {
var cmd: String = required(executable) +
optional("-t", nCoresRequest) +
--
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