Fix pipeline without framework

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-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/GatkVariantcalling.scala

@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
-import nl.lumc.sasc.biopet.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
 import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
-import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

@@ -11,7 +11,7 @@ import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

protected/biopet-protected-package/pom.xml

@@ -30,7 +30,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala

@@ -5,7 +5,8 @@
  */
 package nl.lumc.sasc.biopet
 
-import nl.lumc.sasc.biopet.core.{BiopetExecutable, MainCommand}
+import nl.lumc.sasc.biopet.core.BiopetExecutable
+import nl.lumc.sasc.biopet.utils.MainCommand
 
 object BiopetExecutableProtected extends BiopetExecutable {
   def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(

public/bam2wig/pom.xml

@@ -37,7 +37,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
     </dependencies>

public/bammetrics/pom.xml

@@ -35,7 +35,12 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetToolsExtensions</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 import nl.lumc.sasc.biopet.scripts.CoverageStats
-import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
 import org.broadinstitute.gatk.queue.QScript
 
 class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
-import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
 
 class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 import nl.lumc.sasc.biopet.scripts.CoverageStats
-import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

public/basty/pom.xml

@@ -42,7 +42,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -25,7 +25,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.MultiSampleQScript
 import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
 import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
-import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
+import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 
 trait BastyTrait extends MultiSampleQScript {

public/biopet-core/pom.xml

@@ -41,6 +41,12 @@
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue</artifactId>
             <version>3.4</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.broadinstitute.gatk</groupId>
+                    <artifactId>gsalib</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>

public/biopet-public-package/pom.xml

@@ -41,7 +41,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

@@ -15,7 +15,8 @@
  */
 package nl.lumc.sasc.biopet
 
-import nl.lumc.sasc.biopet.core.{BiopetExecutable, MainCommand}
+import nl.lumc.sasc.biopet.core.BiopetExecutable
+import nl.lumc.sasc.biopet.utils.MainCommand
 
 object BiopetExecutablePublic extends BiopetExecutable {
   def publicPipelines: List[MainCommand] = List(

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala

@@ -47,7 +47,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
   }
 }
 
-object Seqstat {
+object SeqStat {
   def apply(root: Configurable, input: File, output: File): SeqStat = {
     val seqstat = new SeqStat(root)
     seqstat.input = input

public/carp/pom.xml

@@ -35,7 +35,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/flexiprep/pom.xml

@@ -35,7 +35,12 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetToolsExtensions</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -15,11 +15,11 @@
  */
 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
+import nl.lumc.sasc.biopet.extensions.{ Pbzip2, Zcat, Gzip, Sickle }
+import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -19,8 +19,8 @@ import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
-import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
 import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 
 class FlexiprepReport(val root: Configurable) extends ReportBuilderExtension {
   val builder = FlexiprepReport

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -20,7 +20,7 @@ import java.io.File
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Sickle, Zcat }
-import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

public/gears/pom.xml

@@ -32,7 +32,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

@@ -16,7 +16,6 @@
 package nl.lumc.sasc.biopet.pipelines.gears
 
 import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.FullVersion
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.Ln
@@ -25,7 +24,7 @@ import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDupli
 import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.tools.FastqSync
+import nl.lumc.sasc.biopet.extensions.tools.FastqSync
 import org.broadinstitute.gatk.queue.QScript
 
 import scala.collection.JavaConversions._

public/gentrap/pom.xml

@@ -33,11 +33,6 @@
     <name>Gentrap</name>
 
     <dependencies>
-        <dependency>
-            <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
-            <version>${project.version}</version>
-        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Mapping</artifactId>

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -29,7 +29,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
 import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.function.QFunction

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala

@@ -18,10 +18,11 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.extensions.varscan.Mpileup2cns
-import nl.lumc.sasc.biopet.extensions.{ Bgzip, PythonCommandLineFunction, Tabix }
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.language.reflectiveCalls

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 import java.io.{ File, FileOutputStream }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/kopisu/pom.xml

@@ -35,7 +35,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
     </dependencies>

public/mapping/pom.xml

@@ -35,7 +35,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
-import nl.lumc.sasc.biopet.tools.FastqSplitter
+import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping.scripts
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, SortSam }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.{ Cutadapt, Fastqc, SeqtkSeq }
-import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

public/pom.xml

@@ -25,7 +25,7 @@
     <version>0.5.0-SNAPSHOT</version>
     
     <modules>
-        <module>biopet-framework</module>
+        <!--<module>biopet-framework</module>-->
         <module>biopet-public-package</module>
         <module>bammetrics</module>
         <module>flexiprep</module>

public/sage/pom.xml

@@ -35,7 +35,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -22,8 +22,8 @@ import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
 import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.tools.SquishBed
-import nl.lumc.sasc.biopet.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
+import nl.lumc.sasc.biopet.extensions.tools.SquishBed
+import nl.lumc.sasc.biopet.extensions.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 

public/shiva/pom.xml

@@ -32,7 +32,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.report._
-import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -15,18 +15,16 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.File
-
 import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.extensions.delly.Delly
-import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.Input
+
 import scala.collection.JavaConversions._
 
 /**
@@ -70,7 +68,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   def biopetScript(): Unit = {
     for (cal <- configCallers) {
       if (!callersList.exists(_.name == cal))
-        BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
+        Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
     }
 
     val callers = callersList.filter(x => configCallers.contains(x.name))

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -18,13 +18,13 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import org.broadinstitute.gatk.queue.function.CommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -62,7 +62,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
   def biopetScript(): Unit = {
     for (cal <- configCallers) {
       if (!callersList.exists(_.name == cal))
-        BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
+        Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
     }
 
     val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -21,7 +21,7 @@ import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
 import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
-import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -21,7 +21,7 @@ import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.Freebayes
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

public/toucan/pom.xml

@@ -35,7 +35,12 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetFramework</artifactId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetToolsExtensions</artifactId>
             <version>${project.version}</version>
         </dependency>
     </dependencies>

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
-import nl.lumc.sasc.biopet.tools.{ VcfWithVcf, VepNormalizer }
+import nl.lumc.sasc.biopet.extensions.tools.{ VcfWithVcf, VepNormalizer }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript