From 4e14ca721b8cc07e8d63bd39019ba72cb2a4f4f4 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 12 Jun 2014 14:39:31 +0200
Subject: [PATCH] Rename directories and package identifiers for consistency
with Queue
---
.../nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala | 3 ++-
.../nl/lumc/sasc/biopet/core/BiopetQScript.scala | 0
.../{java => scala}/nl/lumc/sasc/biopet/core/Config.scala | 0
.../nl/lumc/sasc/biopet/core/PipelineCommand.scala | 0
.../wrappers => scala/nl/lumc/sasc/biopet/function}/Ln.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/Python.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/Sha1sum.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/Zcat.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/fastq/Cutadapt.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/fastq/Fastqc.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/fastq/Sickle.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 4 ++--
.../sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala | 2 +-
.../biopet/pipelines/flexiprep/scripts/FastqcToContams.scala | 2 +-
.../biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala | 2 +-
.../sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala | 2 +-
.../sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 4 ++--
.../pipelines/gatk/modules/BiopetVariantAnnotator.scala | 0
.../nl/lumc/sasc/biopet/function}/aligners/Bwa.scala | 2 +-
.../nl/lumc/sasc/biopet/function}/aligners/Star.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 4 ++--
22 files changed, 22 insertions(+), 21 deletions(-)
rename biopet-framework/src/main/{java => scala}/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala (99%)
rename biopet-framework/src/main/{java => scala}/nl/lumc/sasc/biopet/core/BiopetQScript.scala (100%)
rename biopet-framework/src/main/{java => scala}/nl/lumc/sasc/biopet/core/Config.scala (100%)
rename biopet-framework/src/main/{java => scala}/nl/lumc/sasc/biopet/core/PipelineCommand.scala (100%)
rename biopet-framework/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/Ln.scala (94%)
rename biopet-framework/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/Python.scala (97%)
rename biopet-framework/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/Sha1sum.scala (94%)
rename biopet-framework/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/Zcat.scala (94%)
rename flexiprep/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/fastq/Cutadapt.scala (98%)
rename flexiprep/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/fastq/Fastqc.scala (98%)
rename flexiprep/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/fastq/Sickle.scala (98%)
rename flexiprep/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala (99%)
rename flexiprep/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala (96%)
rename flexiprep/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala (96%)
rename flexiprep/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala (95%)
rename flexiprep/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala (96%)
rename flexiprep/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala (96%)
rename gatk/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala (99%)
rename gatk/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala (100%)
rename mapping/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/aligners/Bwa.scala (97%)
rename mapping/src/main/{java/nl/lumc/sasc/biopet/wrappers => scala/nl/lumc/sasc/biopet/function}/aligners/Star.scala (98%)
rename mapping/src/main/{java => scala}/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala (99%)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
similarity index 99%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
index 00362623a..6f7744511 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
@@ -1,5 +1,6 @@
- /*
+/*
* Copyright (c) 2012 The Broad Institute
+* Modifications (c) 2014 Leiden University Medical Center
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
similarity index 100%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQScript.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Config.scala
similarity index 100%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Config.scala
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
similarity index 100%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
similarity index 94%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
index a9371cb61..b6d6cbc00 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.InProcessFunction
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala
similarity index 97%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala
index 5bda85e17..90eaca4fb 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.function
import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
similarity index 94%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
index 2dded92c2..a3b546a5e 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
similarity index 94%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
index 206d4bd0d..33b407671 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
similarity index 98%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
index c4c407ec3..ca436d089 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers.fastq
+package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
similarity index 98%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index 36e2e16d7..16c4b9d9e 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers.fastq
+package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
similarity index 98%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
index b8a9d5335..92a098a50 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers.fastq
+package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
similarity index 99%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index c46e4f14b..876fa8cac 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -1,8 +1,8 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.wrappers._
-import nl.lumc.sasc.biopet.wrappers.fastq._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.fastq._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard._
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
similarity index 96%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
index 3defa15fc..3180785a3 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
//import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.wrappers._
+import nl.lumc.sasc.biopet.function._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
similarity index 96%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
index a0c4e9ff2..1ab9b00b5 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
similarity index 95%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
index 346d88d90..da7594b5c 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
similarity index 96%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
index b046872d2..7e6a4c094 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
similarity index 96%
rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
index 2375ffaff..a25832abe 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
similarity index 99%
rename from gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
rename to gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index a0402a2b2..8b4c32e5a 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -1,7 +1,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
-import nl.lumc.sasc.biopet.wrappers._
-import nl.lumc.sasc.biopet.wrappers.aligners._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.aligners._
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.mapping._
import nl.lumc.sasc.biopet.pipelines.flexiprep._
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala b/gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala
similarity index 100%
rename from gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala
rename to gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
similarity index 97%
rename from mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
rename to mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
index f6a5e70f1..d1dae66e3 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers.aligners
+package nl.lumc.sasc.biopet.function.aligners
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
similarity index 98%
rename from mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
rename to mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
index 54e2928fc..492c0413b 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers.aligners
+package nl.lumc.sasc.biopet.function.aligners
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
similarity index 99%
rename from mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
rename to mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index bd774d431..d8174acac 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -1,7 +1,7 @@
package nl.lumc.sasc.biopet.pipelines.mapping
-import nl.lumc.sasc.biopet.wrappers._
-import nl.lumc.sasc.biopet.wrappers.aligners._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.aligners._
import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.flexiprep._
--
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