Omnibus PR

[charles-cowart]

Includes:

• production hotfixes
• job_completed sentinel file creation
• MultiQCJob is now a Slurm job
• MultiQCJob and FastQCJob now use jinja2 templates.

Tests are WIP.

[coveralls]

Pull Request Test Coverage Report for Build 13522577242

Details

• 233 of 266 (87.59%) changed or added relevant lines in 14 files are covered.
• 7 unchanged lines in 6 files lost coverage.
• Overall coverage increased (+0.3%) to 79.874%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
sequence_processing_pipeline/ConvertJob.py	0	1	0.0%
sequence_processing_pipeline/TRIntegrateJob.py	0	1	0.0%
sequence_processing_pipeline/TellReadJob.py	0	1	0.0%
sequence_processing_pipeline/FastQCJob.py	21	23	91.3%
sequence_processing_pipeline/Job.py	4	6	66.67%
sequence_processing_pipeline/NuQCJob.py	12	14	85.71%
sequence_processing_pipeline/SeqCountsJob.py	0	2	0.0%
sequence_processing_pipeline/GenPrepFileJob.py	4	7	57.14%
sequence_processing_pipeline/tests/test_MultiQCJob.py	73	78	93.59%
sequence_processing_pipeline/MultiQCJob.py	87	101	86.14%

Files with Coverage Reduction	New Missed Lines	%
sequence_processing_pipeline/ConvertJob.py	1	85.17%
sequence_processing_pipeline/FastQCJob.py	1	86.06%
sequence_processing_pipeline/NuQCJob.py	1	61.02%
sequence_processing_pipeline/TellReadJob.py	1	56.64%
sequence_processing_pipeline/TRIntegrateJob.py	1	56.41%
sequence_processing_pipeline/SeqCountsJob.py	2	78.71%

Totals
Change from base Build 12711409023:	0.3%
Covered Lines:	2954
Relevant Lines:	3433

---

💛 - Coveralls

[antgonza]

Ready to review or still WIP?

[charles-cowart]

Ready to review or still WIP?

@antgonza Ready for review! ty!

[antgonza]

Just one question.

[wasade]

Please do not merge yet. I have a partial review which I expect to complete later today