schema.json

{
  "pipeline": "Base schema",
  "params": {
    "Pipeline options": {
      "indir": {
        "required": true,
        "help_text": "Directory with isolates to annotate"
      },
      "outdir": {
        "default": "pannotator_results",
        "help_text": "Directory to save results to"
      },
      "bakta_db": {
        "default": "bakta_db/light",
        "help_text": "Path to the Bakta database. If doesn't exist under given path, the 'light' database will be automatically downloaded"
      },
      "bakta_db_type": {
        "default": "light",
        "help_text": "Type of Bakta database to be downloaded. Note that pseudogene detection happens only with the 'full' database [light|full]"
      }
    },
    "Annotation option": {
      "user_proteins": {
        "help_text": "User-provided expert proteins in FASTA format for CDS annotation"
      },
      "user_hmms": {
        "help_text": "User-provided hidden markov model in HMMER format for CDS annotation"
      }
    },
    "Input/output options": {
      "auxiliary_db": {
        "help_text": "Path to a pangenome index to save CDS annotations to. If an index already exists, it will be used to fetch protein annotations, bypassing the standard pipeline"
      },
      "extend_auxdb": {
        "default": "false",
        "help_text": "Add CDS annotations to an existing pangenome JSON index"
      }
    },
    "Logging options": {
      "monochrome_logs": {
        "default": "false",
        "help_text": "Should logs appear in plain ASCII"
      }
    }
  },
  "overwrite_param": {
    "none": {}
  }
}