Fix improper list type check in Toucan

This is a fix for #341 

Perhaps also for @a.h.b.bollen to take a look :).

See merge request !398

Feature cnvpipeline

Work in progress

* [ ] - ConiferExome
* [ ] - ConiferExome Testing
* [x] - FreeC
* [ ] - FreeC testing
* [ ] - cnMOPS
* [ ] - cnMOPS testing
* [ ] - TITAN

Moved to next release:

* [ ] - HMMCopy
* [ ] - HMMCopy testing

See merge request !100

Feature allow custom adapters

fixes #266 

See merge request !384

enableRCtrimming is used to enable trimming of Reverse Complement versions of adapters

Make trimming of Reverse complement version of adapters optional (by default enableRCtrimming=false)

See merge request !393

Added scattering on annotation

Fixes #305 and #324 

See merge request !374

Conflicts:
	flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala

Fixed tagged files

Fixes #339 

See merge request !394

Adding more unit tests

Adding some random unit tests on this branch

Also fixes #338 

See merge request !391

Fix gvcfs extract



See merge request !389