Updates based on testing

[charles-cowart]

No description provided.

[charles-cowart]

@antgonza These are the latest updates from testing on qiita-rc. The PR is deceptively large as all of the changes are relatively small but it's across the board and the tests were adjusted as appropriate.

[coveralls]

Pull Request Test Coverage Report for Build 12458288441

Details

• 126 of 183 (68.85%) changed or added relevant lines in 10 files are covered.
• 5 unchanged lines in 2 files lost coverage.
• Overall coverage decreased (-1.1%) to 79.262%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
sequence_processing_pipeline/SeqCountsJob.py	58	62	93.55%
sequence_processing_pipeline/Commands.py	11	17	64.71%
sequence_processing_pipeline/GenPrepFileJob.py	5	20	25.0%
sequence_processing_pipeline/TRIntegrateJob.py	4	20	20.0%
sequence_processing_pipeline/TellReadJob.py	4	20	20.0%

Files with Coverage Reduction	New Missed Lines	%
sequence_processing_pipeline/TRIntegrateJob.py	1	56.9%
sequence_processing_pipeline/tests/test_Job.py	4	93.49%

Totals
Change from base Build 12146228444:	-1.1%
Covered Lines:	2756
Relevant Lines:	3227

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💛 - Coveralls