Merge branch 'refactor_core-funcs' into 'master'

...n/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

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

...work/src/main/scala/nl/lumc/sasc/biopet/core/Config.scala

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

...work/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala

.../src/main/scala/nl/lumc/sasc/biopet/function/Python.scala

...src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala

...rk/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala

...n/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

...ain/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

...ain/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala

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

...c/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala

.../biopet/pipelines/flexiprep/scripts/FastqcToContams.scala

...biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala

...umc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala

...c/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala

...iopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala

...ain/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala