Software version update
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bakta (1.9.2 -> 1.9.4)
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ncbi-amrfinderplus ( 3.11.18 -> 3.12.8)
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Tbprofiler (5.0.1 to 6.2.1)
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AMRFinderPlus Database Issue: Recently, Pathogenseq failed due to a schema change in the AMRFinderPlus database. This issue occurred because the database was being updated to the latest version each time we run the amrfinderplus program, while the program itself had not been updated to match the new schema. To resolve this, I’ve added a database path to the program. When a specific database path is provided, AMRFinderPlus will no longer attempt to download the database automatically. This change gives us better control over which database versions are used.
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TBProfiler Update (v5.0.1 → v6.2.1): After updating TBProfiler to version 6.2.1, it no longer generates the expected JSON file. This caused an error message stating that the tbprofiler_illumina.json file was missing. I’ve updated the TBProfiler collate module in Pathogenseq v1.3.1 to fix this issue, and the error message should no longer appear.