diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index b40c2b25a2c74862a518b14509d9515f65b3dfcb..61720267c22d49ca94f00d197adbcb31ab44f5ae 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -34,7 +34,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
     this.checkExecutable
     if (contaminants == null) {
       val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
-      contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+      val defaultContams = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+      contaminants = config("contaminants", default = defaultContams)
     }
   }