diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala index ec6623107b338a92766a5884dba4e245dc11cb20..d8149c96d29f2a693548d2c8b63a2e0aa5df84f2 100644 --- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala +++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala @@ -23,6 +23,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable import scala.sys.process.{ Process, ProcessLogger } /** + * Trait for rscripts, can be used to execute rscripts locally + * * Created by pjvanthof on 13/09/15. */ trait Rscript extends Configurable { @@ -42,12 +44,11 @@ trait Rscript extends Configurable { script = script.getAbsoluteFile } else { val rScript: File = dir match { - case Some(dir) => new File(dir, script.getName) - case _ => { + case Some(d) => new File(d, script.getName) + case _ => val file = File.createTempFile(script.getName, ".R") file.deleteOnExit() file - } } if (!rScript.getAbsoluteFile.getParentFile.exists) rScript.getParentFile.mkdirs