Fix smallrna defaultsettings

Change settings to validated settings (by Peter Bram)

See merge request !424

Raise memory

Fixes #356 

- [x] Check Flexiprep
- [x] Check Toucan
- [x] Check Shiva
- [x] Check Mapping
- [x] Check Gears

See merge request !421

Fixed sample and library check

Fixes #357 

See merge request !423

Feature sync stats report

Fixes #312 

See merge request !422

Add hisat2 support

This is for issue #301 

See merge request !419

Switch to Queue 3.6

Fixes #335 and biopet/Biopet-FunctionalTests#25

See merge request !420

Added bedtools sorted flag as default

@a.h.b.bollen: This is for you, can you test is this uses less memory then?

See merge request !395

Extract impute to vcf as separated pipeline



See merge request !413

fixed a config value



See merge request !417

Fix star mapping keep unmapped reads in bamfile

An addition of a config value to the `Mapping` pipeline. Let Star output unmapped reads.

See merge request !416