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This repository was archived by the owner on Apr 22, 2025. It is now read-only.

Omnibus PR #163

Merged
merged 13 commits into from
Mar 3, 2025
Merged

Omnibus PR #163

merged 13 commits into from
Mar 3, 2025

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charles-cowart
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@charles-cowart charles-cowart commented Jan 30, 2025

Includes:

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

Tests are WIP.

@charles-cowart charles-cowart mentioned this pull request Feb 21, 2025
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coveralls commented Feb 21, 2025

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

💛 - Coveralls

@charles-cowart charles-cowart changed the title WIP: Production hotfixes WIP: Omnibus PR Feb 21, 2025
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Ready to review or still WIP?

@charles-cowart charles-cowart changed the title WIP: Omnibus PR Omnibus PR Feb 22, 2025
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charles-cowart commented Feb 22, 2025

Ready to review or still WIP?

@antgonza Ready for review! ty!

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Just one question.

@wasade
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wasade commented Feb 22, 2025

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

@antgonza antgonza merged commit c321054 into qiita-spots:master Mar 3, 2025
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4 participants