Build a table of local genome file paths and write to DuckDB

Source: R/data_curation.R

Scans <base_dir>/data/<bug_dir>/genomes for *.PATRIC.gff, *.fna, *.PATRIC.faa, verifies size > 100 bytes, assembles rows per genome, and writes to the per-bug DuckDB table "files". This writes a Panaroo input file at: <base_dir>/data/<bug_dir>/.txt

genomeList(base_dir = ".", user_bacs, verbose = TRUE)

Arguments

base_dir

Character. Project root.

user_bacs

Character vector. Used to locate per-bug directories and DB.

verbose

Logical. If TRUE, prints messages.

Value

A list with duckdbConnection and table_name = "files".