Fix remove temp files

I did see a lot of temp files that where not removed after testing. This will remove all temp files on exit of a tool / test.

See merge request !238

Fix summary when --sample flag is used in multisample pipelines

Fixes #206 

See merge request !237

Add et option to gatk jobs

Added the et option to gatk.

@a.h.b.bollen: could you maybe test this? I don't have a key

See merge request !169

Fix report

Fixes #202 

See merge request !236

Feature external examples

Added some examples how to make a pipeline and maven artefact that will use biopet, like Magpie 2.0.

Added this as part of #134 

See merge request !227

(cherry picked from commit 5f7b2cbe)

(cherry picked from commit a715d472)

Feature split modules

Fix for #197 and #203 

See merge request !235