Trimmomatic wrapper does not catch java exception

[AsierGonzalez]

Trimmomatic wrapper does not catch java exception

[pjbriggs]

Hello @AsierGonzalez and @AjitPS

Thanks for the detailed report and suggested fix, what you say sounds right to me.

What would be really useful is if you have a small example which can cause the kind of Java-based error condition that you describe. It should then be possible to incorporate as a new test case (I gather it's now possible to make test cases that are expected to fail using expect_failure="true" in the <test> case, although I have yet to try this). Would you be able to make one that we can use?

Either way if you'd like to make a PR with the changes then please go ahead and we can take it from there.

Thanks for your interest in the Trimmomatic tool.

Peter