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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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[SRA_Fetch] When re-running workflow, any warnings are not overwritten #453

Closed emmadoughty closed 5 months ago

emmadoughty commented 5 months ago

:bug:

:pencil: Describe the Issue

When you re-run the workflow for samples where the SRA lite format has been detected, there's nothing to overwrite the warning column so it remains, even though the fastqs are probably not in SRA lite format (though there's now no way to tell).

:repeat: How to Reproduce

Run SRA_fetch and download FASTQs in SRA lite format, then re-run the wf

:fishing_pole_and_fish: Expected Behavior

Warning column gets populated with confirmation of no warning

:floppy_disk: Version Information

v2.0.0

:information_source: Additional Information

sage-wright commented 5 months ago

Tests show warning column does get overwritten with blank values when not SRA lite; SRA lite format was likely detected again.