From c0f8f2a37cf0f7643543a0a5d567fc99d7a7c7d4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 19 Sep 2016 14:32:04 +0200
Subject: [PATCH] Added executables to testing
---
.../nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala | 2 +-
.../sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala | 2 ++
3 files changed, 4 insertions(+), 2 deletions(-)
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 2164a195b..2c54fdd2a 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 cd8ff0be9..dd87ce906 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 de2cc5a03..943fba618 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"),
--
GitLab