Merge remote-tracking branch 'origin/develop' into feature-pipeable

Conflicts:
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala

protected/biopet-gatk-extensions/pom.xml

@@ -25,7 +25,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
 }

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
   scatterCount = config("scattercount", default = 0)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
   annotation ++= config("annotation", default = Seq("FisherStrand", "QualByDepth", "ChromosomeCounts")).asStringList

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {
   if (config.contains("scattercount")) scatterCount = config("scattercount")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
   override def beforeGraph() {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 
 class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantRecalibrator with GatkGeneral {

protected/biopet-gatk-pipelines/pom.xml

@@ -25,7 +25,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

@@ -6,7 +6,7 @@
 package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
 import org.broadinstitute.gatk.queue.QScript
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import org.broadinstitute.gatk.queue.QScript
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
 import org.broadinstitute.gatk.queue.QScript