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Need to modify populate_fields() function assert statement to allow valid strings and not only "" or "Not Provided"
Run environment (container, cloud service, HPC, platform, etc.)
Any
Command to replicate the error:
nextflow run main.nf -profile test,singularity --species bacteria --output_dir test_bact --submission_config ~/02.scratch/submission_config.yaml --bakta_db_path /scicomp/reference/bakta/db
Any Additional Context or Information?
This mistake got missed with viral test data because all the terms_2_replace were missing. In bacteria test data, isolation_source = "Clinical," which is a valid string that was getting caught in the incorrect assert statement.
The text was updated successfully, but these errors were encountered:
Need to modify populate_fields() function assert statement to allow valid strings and not only "" or "Not Provided"
Run environment (container, cloud service, HPC, platform, etc.)
Any
Command to replicate the error:
nextflow run main.nf -profile test,singularity --species bacteria --output_dir test_bact --submission_config ~/02.scratch/submission_config.yaml --bakta_db_path /scicomp/reference/bakta/db
Any Additional Context or Information?
This mistake got missed with viral test data because all the terms_2_replace were missing. In bacteria test data, isolation_source = "Clinical," which is a valid string that was getting caught in the incorrect assert statement.
The text was updated successfully, but these errors were encountered: