| 294 | |
| 295 | |
| 296 | def r_command(args: argparse.Namespace, run_dir: Path, method: dict[str, Any]) -> list[str]: |
| 297 | return [ |
| 298 | "Rscript", |
| 299 | "workflow/scripts/run_bulk_de.R", |
| 300 | str(args.count_matrix.expanduser().resolve()), |
| 301 | str(args.sample_metadata.expanduser().resolve()), |
| 302 | str(args.contrasts.expanduser().resolve()), |
| 303 | str(method.get("selected_method", "limma_log2")), |
| 304 | str(method.get("input_mode", "normalized_expression")), |
| 305 | str(method.get("fit_formula", "~ 0 + condition")), |
| 306 | str(run_dir), |
| 307 | ] |
| 308 | |
| 309 | |
| 310 | def write_commands(run_dir: Path, cmd: list[str]) -> None: |