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Replace homemade annotation script with W4M's lcmsmatching #12

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elliotfontaine opened this issue Jun 11, 2024 · 1 comment
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help wanted Extra attention is needed type:feature New feature or request
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@elliotfontaine
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https://github.com/workflow4metabolomics/lcmsmatching

Steps:

  • Test lcmsmatching with our data and discover its interface.
  • Compare results.
  • Compare speed.
  • Implement it in a task, with additional table formatting if necessary.
@elliotfontaine elliotfontaine added the type:feature New feature or request label Jun 11, 2024
@elliotfontaine elliotfontaine self-assigned this Jun 11, 2024
@elliotfontaine elliotfontaine added this to the 0.1.0 milestone Jun 11, 2024
@elliotfontaine
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See discussion in workflow4metabolomics/lcmsmatching#68.

Replacing the mzmatch junk script used by our workflow by the lcmsmatching R script won't be straightforward. The latter doesn't work with current versions of its core dependency biodb.
One approach would be to partially reimplement lcmsmatching using biodb 1.10.0, and following what's inside vignettes:

@elliotfontaine elliotfontaine added the help wanted Extra attention is needed label Jul 19, 2024
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