Merge branch 'feature-input_files_checking' into develop

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

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

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

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

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

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

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala

...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

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