Output

The pipeline produces the following output directory structure:

results/
├── bakta/
│   └── <sample>/
│       ├── <prefix>.gff3       # GFF3 annotation
│       ├── <prefix>.gbff       # GenBank annotation
│       ├── <prefix>.fna        # Annotated nucleotide sequences
│       ├── <prefix>.ffn        # Feature nucleotide sequences
│       ├── <prefix>.faa        # Translated CDS sequences
│       ├── <prefix>.tsv        # Tab-separated annotation summary
│       ├── <prefix>.json       # Machine-readable JSON annotation
│       ├── <prefix>.txt        # Human-readable annotation summary
│       ├── <prefix>.png        # Genome plot (optional)
│       └── <prefix>.svg        # Genome plot (optional)
├── eggnog/
│   └── <sample>/
│       ├── <prefix>.emapper.annotations    # Functional annotations
│       ├── <prefix>.emapper.seed_orthologs # Seed ortholog matches (optional)
│       ├── <prefix>.emapper.hits           # Search hits (optional)
│       └── <prefix>.emapper.orthologs      # Ortholog assignments (optional)
└── pipeline_info/
    ├── timeline_<timestamp>.html
    ├── report_<timestamp>.html
    ├── trace_<timestamp>.txt
    └── dag_<timestamp>.html

bakta/

Full Bakta annotation output for each sample. Which annotation features are run is controlled by the skip flags in conf/advanced.config.

eggnog/

When --eggnog_run true (default), eggNOG-mapper runs on Bakta-generated protein FASTA files (*.faa) for each sample using the diamond search mode. The annotations are written as *.emapper.* files under each sample directory.

pipeline_info/

Nextflow execution reports: timeline, resource usage, trace log, and DAG visualization.