Run the minibwa CLI — minibwa_cli • Rminibwa

Low-level helper for invoking arbitrary minibwa commands from R. Prefer minibwa_index() and minibwa_map() for common workflows.

Usage

minibwa_cli(args = character(), stdout = TRUE, path = minibwa_path())

Arguments

args: Character vector of command-line arguments passed to minibwa.
stdout: Passed to system2(). Use TRUE to capture standard output, FALSE to inherit it, or a file path to redirect it.
path: Executable name or path.

Value

If stdout = TRUE, a character vector of captured output; otherwise an invisible process status.