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@an-altosian an-altosian commented Aug 17, 2025

  1. move the RANK_GENES_GROUPS module into the DIFFERENTIAL_EXPRESSION subworkflow.
  2. do DE for both leiden clustering results and cell types detected.
  3. modified LEIDEN, SINGLER and CELLTYPIST modules to make them write the cell labels into a cvs file, and do DE based on these files.
  4. tested using the test profile.

TODO:

  1. I am not familiar with multiQC so I skipped that part.
  2. nf-core test needs to be updated.

@nictru
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nictru commented Aug 17, 2025

Hey, just to let you know, I am currently on vacation and will look into this after that

@an-altosian
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Haha no worries at all! I was just too excited to stop coding yesterday. Maybe we can have a kick-off meeting when you come back from your vacation, because I modified a quite big amount of chunks of code.

Have fun!

Best,
Dongze

@nictru nictru self-requested a review August 29, 2025 07:40
@an-altosian
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Hi @nictru , I think this PR is ready. Please let me know if you want me to explain this further!

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2 participants