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juliencarponcy / trialexp

MIT License
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Spike sorting minor fix #18

Closed teristam closed 1 year ago

teristam commented 1 year ago

This PR contains some minor fixes for the spike sorting branch

  1. Move all configurations into one env file, so that it is easier to change them. Also, using env variables allow us to just set them in the running machine directly, allowing different users to run the same script (different user may have different mount location)
  2. Change the folder output of the sorting slightly so that spikeinterface won't complain about existing folders. The output folder for sorting and the one we use to save the sorting extractor should be in different folders.
  3. Reorganize the rule dependencies in the sorting snakefile so that the input function is in the last step, so that it can give a more accurate estimation of the number of sorting that needs to be run in the snakemake stats.