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add bidcell subworkflow#78

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add bidcell subworkflow#78
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@an-altosian an-altosian commented Apr 27, 2025

The first draft of the bidcell workflow proposed in #17

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an-altosian commented Apr 29, 2025

The python script, module, and subworkflow is basically done. I have tested it using the latest version of xenium bundle.

Caveats:

  1. BIDCell has to run with GPU, so we might need to add some prechecks to ensure GPU is accessible.
  2. It uses DAPI focused image (morphology_mip.ome.tif or morphology_focus/morphology_focus_0000.ome.tif) instead of the Z-stack one (morphology.ome.tif).
  3. It takes a single channel containing both the bundle and the ref as the input. It output the entire output folder. I will adjust this once know more about what the downstream modules take.
  4. If no ref is provided, it will use a dummy ref provided in BIDCell github repo and set the weight of positive and negative markers as zero.
  5. If no elongated cell types are provided, it will add a dummy one called placeholder to the ref because otherwise BIDCell complains.

@an-altosian an-altosian marked this pull request as ready for review April 29, 2025 20:51
@khersameesh24 khersameesh24 added enhancement New feature or request prio3 labels May 4, 2025
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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