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SpatialHackathon / SpaceHack2023

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BUGS fixed when tried pipeline #207

Closed Jieran-S closed 9 months ago

Jieran-S commented 9 months ago

Hi! Please review this PR to see if it makes sense. Many bugs found when I tried to run our workflow:

  1. method/BayesSpace/BayesSpace.r and method/SpiceMix/SpiceMix.py: Their shell argument input are not the same as template method files, leading to smk crash. (for instance, SpiceMix doesn't provide --technology option before I change the script)

  2. method/GraphST/GraphST_optargs.json, method/SpaceFlow/spaceflow_optargs.json: Both of their preprocessing workflows have PCA procedures, but downstream only use scaled data and I can't find anywhere for using PCA. (Question: can we provide scaled data as transform data?) Fixed issue #209

  3. templates/method.py: Fixed a typo.

There're some more bugs that need to be discussed. I'll open issues.

Jieran-S commented 9 months ago

method/scanpy/method_scanpy.py: Update output format so the column name will be "label"

Jieran-S commented 9 months ago

method/SOTIP/method_sotip.py: commit to fix issue #208