nf-core/pathogensurveillance
FIND_ASSEMBLIES returns error code when no results are found
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#133 aberto em 14 de jan. de 2025
buggood first issue
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Description
This is low priority, since it does not prevent the pipeline for functioning correctly.
If a taxon is supplied for which there is no data, the following output is produced by datasets summary genome taxon --as-json-lines pseudeurotiaceae > Pseudeurotiaceae.json:
Error: The taxonomy name 'pseudeurotiaceae' (taxid: '34379') is valid, but no genome data is currently available for this taxon.
Use datasets summary genome taxon <command> --help for detailed help about a command.
The exitcode returned is 1, which makes nextflow think the process failed and it retries. In this case, it actually worked, there is just no data, so ideally it would return an exit code of 0 and an empty JSON file. A check should be added to modules/local/find_assemblies.nf for the phrase "is valid, but no genome data is currently available for this taxon" and make an empty JSON file and return exit code 0.