Update BV-BRC metadata in DuckDB

Fetches bacterial genome metadata from BV-BRC using the BV-BRC CLI and stores it in a DuckDB database under data/bvbrc/bvbrcData.duckdb within base_dir. If the table exists and is older than max_age_days, it refreshes; otherwise, loads the existing table. BV-BRC column names are preserved exactly.

.updateBVBRCdata(
  base_dir = ".",
  max_age_days = 30L,
  image = "danylmb/bvbrc:5.3",
  verbose = TRUE
)

Arguments

base_dir

Character. Project root. The DuckDB database is created at file.path(base_dir, "data", "bvbrc", "bvbrcData.duckdb").

max_age_days

Integer. Refresh the table if older than this many days. Default: 30.

image

Character. Docker image used by .fetchBVBRCdata(). Default: "danylmb/bvbrc:5.3".

verbose

Logical. If TRUE, prints informative messages. Default: TRUE.

Value

A tibble containing BV-BRC bacterial genome metadata.