()
| 687 | |
| 688 | |
| 689 | def parse_args() -> argparse.Namespace: |
| 690 | parser = argparse.ArgumentParser(description=__doc__) |
| 691 | parser.add_argument("--sample-sheet", type=Path, required=True) |
| 692 | parser.add_argument("--reference-fasta", type=Path, required=True) |
| 693 | parser.add_argument("--target-bed", type=Path) |
| 694 | parser.add_argument("--panel-of-normals", type=Path) |
| 695 | parser.add_argument("--germline-resource", type=Path) |
| 696 | parser.add_argument("--annotation-vcf", type=Path) |
| 697 | parser.add_argument("--f1r2-orientation-model", action="store_true") |
| 698 | parser.add_argument( |
| 699 | "--genome-build", |
| 700 | help="Genome build or registry alias for resource readiness, e.g. GRCh38, mm39, or a configured local alias.", |
| 701 | ) |
| 702 | parser.add_argument( |
| 703 | "--bundle-root", |
| 704 | action="append", |
| 705 | default=[], |
| 706 | help="Resource bundle override formatted as bundle=/path. May be repeated.", |
| 707 | ) |
| 708 | parser.add_argument("--include-optional-resources", action="store_true") |
| 709 | parser.add_argument("--resource-checksums", action="store_true") |
| 710 | parser.add_argument( |
| 711 | "--require-resource-plan", |
| 712 | action="store_true", |
| 713 | help="Treat missing registered reference bundles as blocking for this direct runner.", |
| 714 | ) |
| 715 | parser.add_argument( |
| 716 | "--skip-resource-plan", |
| 717 | action="store_true", |
| 718 | help="Skip registered reference bundle readiness checks.", |
| 719 | ) |
| 720 | parser.add_argument("--outdir", type=Path) |
| 721 | parser.add_argument("--run-id", default=slug_timestamp("dna-somatic-variants")) |
| 722 | parser.add_argument("--execute", action="store_true") |
| 723 | return parser.parse_args() |
| 724 | |
| 725 | |
| 726 | def serializable_args(args: argparse.Namespace) -> dict[str, Any]: |
no test coverage detected