Fix pipeline without framework

protected/biopet-gatk-extensions/pom.xml

protected/biopet-gatk-pipelines/pom.xml

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

protected/biopet-protected-package/pom.xml

...scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala

public/bam2wig/pom.xml

public/bammetrics/pom.xml

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

public/basty/pom.xml

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

public/biopet-core/pom.xml

public/biopet-public-package/pom.xml

...in/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala

public/carp/pom.xml

public/flexiprep/pom.xml