Updates to support proper function and testing of code in qp-klp.

[coveralls]

Pull Request Test Coverage Report for Build 6856512817

• 61 of 96 (63.54%) changed or added relevant lines in 5 files are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage decreased (-0.6%) to 82.83%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
sequence_processing_pipeline/scripts/cli.py	1	2	50.0%
sequence_processing_pipeline/Commands.py	4	9	44.44%
sequence_processing_pipeline/NuQCJob.py	12	41	29.27%
<!--	Total:	61	96	63.54%	-->

Files with Coverage Reduction	New Missed Lines	%
sequence_processing_pipeline/NuQCJob.py	1	56.33%
<!--	Total:	1		-->

Totals
Change from base Build 6632678122:	-0.6%
Covered Lines:	2107
Relevant Lines:	2408

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💛 - Coveralls

[charles-cowart]

@antgonza Thank you for the review! Testing on qiita-rc with the latest change was successful. Please feel free to merge at your convenience!