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Ingest qc score fix 2 #318

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Ingest qc score fix 2 #318

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wlason
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@wlason wlason commented Nov 6, 2024

I found further problems with the defaults in calc_proportions.

  • I updated the old defaults in run_scanpyQC_rna.py from "mitochondrial,ribosomal" to None
  • Added the if-statement to not process the calc_proportion string if it is not passed
  • Added the new defaults consistent with qc_genelist_1.0.csv to the ingest yaml

@wlason wlason requested review from bio-la and deevdevil88 November 6, 2024 17:24
bio-la
bio-la reviewed Nov 13, 2024
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panpipes/python_scripts/run_scanpyQC_rna.py
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good catch @wlason setting None in the python script will kick in if nothing is specified in the pipeline.yml. (current default in the pipeline.yml is MarkersNeutro but the change you have introduced ensures that None is the intended parameter)

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@deevdevil88 deevdevil88 Awaiting requested review from deevdevil88

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