Fix samples dir gentrap



See merge request !277

Fix docs



See merge request !276

Fixed scala docs in docs



See merge request !275

Feature docs developers 0.5.0

Some fixes to the docs (last minute edits)

See merge request !273

Feature docs 0.5.0

If there is nothing wrong with this we should just merge it to develop.

Thi

See merge request !253

Fix depedencies

This will create a json file what will store job and file dependencies at the start of the pipeline.

See merge request !269

Changes in gsnap piping and fix bug in fastqsync

This is I think a forgotten branch.

@s.a.j.van_der_zeeuw: Is this tested and does this work?

See merge request !270

Added version command for star

Only need to be tested

See merge request !271

Fix gentrap null pointer

Fixes #234 

See merge request !268