This reverts commit 2b618795.

Fixed error message in bamutils

Fixes #259 

See merge request !311

Update Cutadapt wrapper

Updated cutadapt wrapper to reflect cutadapt 1.9 and added missing options (which were already supported in 1.5 but not in extension)

Closes #243 

See merge request !310

Feature core unit tests

Fixes #253 

See merge request !307

Fix renames

Some naming fixes for consistency.

See merge request !309

Feature basic gentrap report

Part of #223 

This only contains basic stats, no gentrap specific stats added.

See merge request !302

Fix spelling error in the WriteDependencies JSON output

Fix the output keys for the JSON output of `writedependencies`.

See merge request !305

Fix short name



See merge request !303

Switch gentrap to multisample mapping

Fixes #256 

See merge request !299