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BU-ISCIII / relecov-tools

set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.
GNU General Public License v3.0
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log_summary creates an excel file from logs #300

Closed Shettland closed 2 months ago

Shettland commented 2 months ago

Now json_validation.py also creates an excel file with the logs from the validation process. The excel file includes two sheets, one with errors and the other one with warnings. Each sheet has three columns, the first corresponds with sequencing_sample_id, the second indicates if the sample was valid or not, and the third is the content of the logs (either errors or warnings, depending on the sheet).

Closes #283

saramonzon commented 2 months ago

This includes only the excel generation for the json validation step? How do you plan to include the warnings and errors arised from download and read metadata lab steps?

Shettland commented 2 months ago

This includes only the excel generation for the json validation step? How do you plan to include the warnings and errors arised from download and read metadata lab steps?

If you want this excel to include logs from other modules I could include this new method in log_summary.py instead