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