From af141f384082d25428e4f443663330610957e707 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 12:45:28 +0200
Subject: [PATCH] Moved to flexiprep maven app

---
 .../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala     | 1 +
 .../java/nl/lumc/sasc/biopet/wrappers/fastq}/Cutadapt.scala     | 2 +-
 .../main/java/nl/lumc/sasc/biopet/wrappers/fastq}/Fastqc.scala  | 0
 .../main/java/nl/lumc/sasc/biopet/wrappers/fastq}/Sickle.scala  | 0
 4 files changed, 2 insertions(+), 1 deletion(-)
 rename {biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers => flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq}/Cutadapt.scala (98%)
 rename {biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers => flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq}/Fastqc.scala (100%)
 rename {biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers => flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq}/Sickle.scala (100%)

diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 554101a2d..1a0173d49 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -2,6 +2,7 @@ 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 org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.extensions.picard._
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
similarity index 98%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
rename to flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
index 0e2ea0174..b9bfbaff2 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Cutadapt.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.wrappers.fastq
 
 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/Fastqc.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
similarity index 100%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Fastqc.scala
rename to flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
similarity index 100%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sickle.scala
rename to flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
-- 
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