SpatialHackathon/SpaceHack2023

Snakemake workflow

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Jieran-S commented

An issue tracking progress for snakemake workflow update.

Progress (14.02.2024)

  1. Download, preprocessing workflow workable
  2. Method workflow workable but without optargs function
  3. All config up-to-date with all methods/metrics/datasets available

Update (19.02.2024)

  1. Metrics optargs and eligibility check included. All modules are technically functional if method/metric implementation is not buggy.
  2. Fixed bugs in SpiceMix, SOTIP, and SpaceFlow that can crash the workflow

Update (22.02.2024)

  1. PAS and CHAOS physical coordinates added.

TODO: (22.02.2024)

  1. Modify resolution to cluster number conversion

  2. methods: parallelization for different preprocessing options

  3. PAS returns bugs. Check reason