()
| 545 | |
| 546 | |
| 547 | def parse_args() -> argparse.Namespace: |
| 548 | parser = argparse.ArgumentParser(description=__doc__) |
| 549 | parser.add_argument("--sample-sheet", type=Path, required=True) |
| 550 | parser.add_argument("--bowtie2-index") |
| 551 | parser.add_argument("--bam-only", action="store_true") |
| 552 | parser.add_argument("--genome-size", required=True) |
| 553 | parser.add_argument("--blacklist-bed", type=Path) |
| 554 | parser.add_argument("--tss-bed", type=Path) |
| 555 | parser.add_argument( |
| 556 | "--genome-build", |
| 557 | help="Genome build or registry alias for resource readiness, e.g. GRCh38, mm39, or a configured local alias.", |
| 558 | ) |
| 559 | parser.add_argument( |
| 560 | "--bundle-root", |
| 561 | action="append", |
| 562 | default=[], |
| 563 | help="Resource bundle override formatted as bundle=/path. May be repeated.", |
| 564 | ) |
| 565 | parser.add_argument("--include-optional-resources", action="store_true") |
| 566 | parser.add_argument("--resource-checksums", action="store_true") |
| 567 | parser.add_argument( |
| 568 | "--require-resource-plan", |
| 569 | action="store_true", |
| 570 | help="Treat missing registered reference bundles as blocking for this direct runner.", |
| 571 | ) |
| 572 | parser.add_argument( |
| 573 | "--skip-resource-plan", |
| 574 | action="store_true", |
| 575 | help="Skip registered reference bundle readiness checks.", |
| 576 | ) |
| 577 | parser.add_argument("--run-motifs", action="store_true") |
| 578 | parser.add_argument("--motif-genome") |
| 579 | parser.add_argument("--motif-size", default="given") |
| 580 | parser.add_argument("--min-mapq", type=int, default=30) |
| 581 | parser.add_argument("--threads", type=int, default=4) |
| 582 | parser.add_argument("--outdir", type=Path) |
| 583 | parser.add_argument("--run-id", default=slug_timestamp("atacseq-peaks-qc")) |
| 584 | parser.add_argument("--execute", action="store_true") |
| 585 | return parser.parse_args() |
| 586 | |
| 587 | |
| 588 | def serializable_args(args: argparse.Namespace) -> dict[str, Any]: |
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