Merge all maven packages into 1

bam-metrics/.gitignore

bam-metrics/nbactions.xml

bam-metrics/pom.xml

biopet-framework/examples/bam-metrics.json

biopet-framework/examples/flexiprep.json

biopet-framework/examples/gatk-benchmark-genotyping.json

biopet-framework/examples/gatk-genotypeing.json

biopet-framework/examples/gatk-pipeline.json

biopet-framework/examples/gatk-variantcalling.json

biopet-framework/examples/gatk-vcf-sample-compare.json

biopet-framework/examples/mapping.json

biopet-framework/pom.xml

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

...n/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala

.../scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala

...cala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala

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

...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala

...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala