Database Requirements

The following databases are required before running the pipeline. All paths must be provided via command-line options or configuration files:

• GTDB-Tk reference database (--gtdbtk_classify_wf_data_path): Taxonomic classification of MAGs.
• CheckM2 database (--binette_checkm2_db): Bin quality assessment in Binette.
• geNomad database (--genomad_db): Viral and plasmid element detection.
• AMRFinderPlus database (--amrfinderplus_db): Antimicrobial resistance gene profiling.

Download all from research.foodsafetyrisk.org.

Once downloaded, uncompress and set UNIX paths in workflows/conf/maggic.config and workflows/conf/maggic_lr.config:

• binette_checkm2_db = /path/to/maggic_dbs/checkm2/latest
• gtdbtk_classify_wf_data_path = /path/to/gtdbtk/release232
• genomad_db = /path/to/maggic_dbs/genomad/latest/genomad_db
• amrfinderplus_db = /path/to/maggic_dbs/amrfinderplus/latest

Setting database paths in the configuration file is the recommended approach, since it avoids specifying them via CLI on every run.