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openpipelines-bio / openpipeline

https://openpipelines.bio
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Add calculate_qc_metrics component to ingestion pipelines #541

Closed ddemaeyer closed 6 months ago

ddemaeyer commented 8 months ago

https://github.com/openpipelines-bio/openpipeline/blob/bc9c07361c06f876b61e07af340902e5cefa0c4b/workflows/ingestion/cellranger_multi/main.nf#L60

For additional QCing we should add the calculation of the qc metrics on the unfiltered object.

The proposal is to add the calculate QC metrics calculation on 2 locations:

  1. Unfiltered to the ingestion pipeline (see reference) Goal: can be used in intermediary reports and visualization
  2. Keep the component in the multisample pipelines for filtered QCing
LucHendriks commented 8 months ago

@rcannood or @DriesSchaumont feel free to reach out to me for details surrounding this issue.

DriesSchaumont commented 6 months ago

I think this issue can be closed with #585, which introduces the qc pipeline.