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>