diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala index 2164a195bee623b03ae04c8f8696ed86353165c8..2c54fdd2a545b9665187f406a0e9e8ca94d12195 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala @@ -19,7 +19,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with var inputR2: Option[File] = None @Input(doc = "Centrifuge index prefix", required = true) - var index: File = config("centrifige_index") + var index: File = config("centrifuge_index") @Output(doc = "Output with hits per sequence") var output: File = _ diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala index cd8ff0be92e3d19585c19d8bd8169ef5b22671dc..dd87ce906c41a6c7b53f572ba8ad3a0b0b0a966f 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala @@ -17,7 +17,7 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio var output: File = _ @Input(doc = "Centrifuge index prefix", required = true) - var index: File = config("centrifige_index", namespace = "centrifuge") + var index: File = config("centrifuge_index", namespace = "centrifuge") executable = config("exe", default = "centrifuge-kreport", freeVar = false) diff --git a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala index de2cc5a0361bbce067cdeacf8f9976e508f40aa7..943fba618c229974f93639279494362bc1c6661e 100644 --- a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala +++ b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala @@ -231,6 +231,8 @@ object TestGearsSingle { val executables = Map( "kraken" -> Map("exe" -> "test", "db" -> "test"), + "centrifuge" -> Map("exe" -> "test", "centrifuge_index" -> "test"), + "centrifugekreport" -> Map("exe" -> "test"), "krakenreport" -> Map("exe" -> "test", "db" -> "test"), "sambamba" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),