Closed LeonHafner closed 3 weeks ago
Currently SOLO as implemented in the local process in this pipeline filters doublets, but then returns the predictions inverted. It returns doubled cells coded with False while non-doublets are coded as True. https://github.com/nf-core/scdownstream/blob/b15c52b8cac3e85862c0a02089119c4571c8b1a8/modules/local/scvitools/solo/templates/solo.py#L71
False
True
Other tools used here like scrublet do it the other (more intuitive way): https://github.com/nf-core/scdownstream/blob/b15c52b8cac3e85862c0a02089119c4571c8b1a8/modules/local/scanpy/scrublet/templates/scrublet.py#L51
This should get fixed as we add the module to nf-core without the bug and import it later as it is available.
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Description of the bug
Currently SOLO as implemented in the local process in this pipeline filters doublets, but then returns the predictions inverted. It returns doubled cells coded with
Falsewhile non-doublets are coded asTrue. https://github.com/nf-core/scdownstream/blob/b15c52b8cac3e85862c0a02089119c4571c8b1a8/modules/local/scvitools/solo/templates/solo.py#L71Other tools used here like scrublet do it the other (more intuitive way): https://github.com/nf-core/scdownstream/blob/b15c52b8cac3e85862c0a02089119c4571c8b1a8/modules/local/scanpy/scrublet/templates/scrublet.py#L51
This should get fixed as we add the module to nf-core without the bug and import it later as it is available.
Command used and terminal output
No response
Relevant files
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System information
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