Database file column `db_name` allows repeated entries bvut should not

[d4straub]

Description of the bug

The verification of the database column db_name seems not to work as intended. Each entry must be unique, as far as I understand, but I was able to use a database file that violates that principle and consequently the pipeline failed.

Potentially that line is not working as intended:

taxprofiler/assets/schema_database.json

Line 58 in fa1aab0

"uniqueEntries": ["tool", "db_name"]

Command used

NXF_VER=25.04.6 nextflow run nf-core/taxprofiler -r 2.0.0 -profile cfc -c resources_taxprofiler.config --input samplesheet_taxprofiler.csv --databases databases_taxprofiler.csv --outdir results_taxprofiler --perform_longread_qc --run_kraken2 --run_bracken --run_profile_standardisation --run_krona -resume

Terminal output

-[nf-core/taxprofiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:taxprofiler:STANDARDISATION_PROFILES:TAXPASTA_MERGE (6)'
Caused by:
  Process `NFCORE_TAXPROFILER:taxprofiler:STANDARDISATION_PROFILES:TAXPASTA_MERGE` input file name collision -- There are multiple input files for each of the following file names: sample13sr_sample13sr_k2_standard_20260226.bracken.tsv, sample14sr_sample14sr_k2_standard_20260226.bracken.tsv, sample19sr_sample19sr_k2_standard_20260226.bracken.tsv

Relevant files

the database file I used:

tool,db_name,db_type,db_params,db_path
kraken2,k2_standard_20260226,,,k2_standard_20260226.tar.gz
bracken,k2_standard_20260226,short,;-r 150,k2_standard_20260226.tar.gz
kraken2,k2_nt_20230502,,,k2_nt_20230502.tar.gz
bracken,k2_nt_20230502,short,;-r 150,k2_nt_20230502.tar.gz
kraken2,k2_core_nt_20251015,,,k2_core_nt_20251015.tar.gz
bracken,k2_core_nt_20251015,short,;-r 150,k2_core_nt_20251015.tar.gz

System information

Version of nf-core/taxprofiler: 2.0.0