Running tests locally generates (or changes?) outputs that are not .gitignored

[vreuter]

After running tests locally, with git status I see...

...
Untracked files:
  (use "git add <file>..." to include in what will be committed)
	tests/Data/pipeline_output/
	tests/Data/pipeline_output3/

no changes added to commit (use "git add" and/or "git commit -a")

[donaldcampbelljr]

Related to this: #185