Init bed check

fixes #298 

See merge request !401

Changes arg parser with getOrElse(throw new IllegalArgumentException)

Fixes #342 

See merge request !402

Fixed fifo job names

Fixes #334 

See merge request !399

# Conflicts:
#	generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala

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

(cherry picked from commit c1d44135)

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