diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala index 59f8fda3c534ce14b85f2d20042cf15a7611101a..ed687bb0be6100db76a887e382d7dda2e709b715 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala +++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala @@ -37,10 +37,10 @@ class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction var sampleName: String = _ override def cmdLine = super.cmdLine + - "-i" + required(input) + - "-n" + required(sampleName) + - "-s" + required(insertsize) + - "-o" + required(output) + required("-i", input) + + required("-n", sampleName) + + required("-s", insertsize) + + required("-o", output) } object PindelConfig extends ToolCommand {