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Handle two quantification table folders of GNPS feature-based workflow #275

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merged 1 commit into from
Sep 17, 2024

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CunliangGeng
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@CunliangGeng CunliangGeng commented Sep 16, 2024

Dora found the following issue:
GNPS FEATURE-BASED-MOLECULAR-NETWORKING workflow might output two folders for quantification table with folder name:

  • quantification_table
  • quantification_table_reformatted
    In this case, NPLinker will raise an error. However, NPLinker is expected to pick one folder and process the data.

This PR changes NPLinker to make it always first pick the quantification_table_reformatted folder, if this folder does not exist, then pick quantification_table folder to process the data. If neither exist, raise an error.

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CunliangGeng commented Sep 16, 2024

@CunliangGeng CunliangGeng self-assigned this Sep 16, 2024
@CunliangGeng CunliangGeng marked this pull request as ready for review September 16, 2024 14:46
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Please ignore the failed tests that are caused by antismash downloading. Tests are good for the changes of this PR. Same for PR #276 and #277.

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CunliangGeng commented Sep 17, 2024

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@CunliangGeng CunliangGeng merged commit b3489a8 into dev Sep 17, 2024
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@CunliangGeng CunliangGeng deleted the fix_gnps_quantification_folder branch September 17, 2024 12:12
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2 participants