()
| 1041 | |
| 1042 | |
| 1043 | def parse_args() -> argparse.Namespace: |
| 1044 | parser = argparse.ArgumentParser(description=__doc__) |
| 1045 | parser.add_argument("--sample-sheet", type=Path, required=True) |
| 1046 | parser.add_argument( |
| 1047 | "--backend", choices=["qiime2", "dada2", "nf-core/ampliseq"], default="qiime2" |
| 1048 | ) |
| 1049 | parser.add_argument("--marker", default="16S") |
| 1050 | parser.add_argument("--primer-forward", required=True) |
| 1051 | parser.add_argument("--primer-reverse", required=True) |
| 1052 | parser.add_argument("--taxonomy-classifier", type=Path) |
| 1053 | parser.add_argument("--metadata", type=Path) |
| 1054 | parser.add_argument("--trunc-len-f", type=int) |
| 1055 | parser.add_argument("--trunc-len-r", type=int) |
| 1056 | parser.add_argument("--sampling-depth", type=int, default=1000) |
| 1057 | parser.add_argument("--threads", type=int, default=4) |
| 1058 | parser.add_argument("--profile") |
| 1059 | parser.add_argument( |
| 1060 | "--bundle-root", |
| 1061 | action="append", |
| 1062 | default=[], |
| 1063 | help="Resource bundle override formatted as bundle=/path. May be repeated.", |
| 1064 | ) |
| 1065 | parser.add_argument( |
| 1066 | "--include-optional-resources", |
| 1067 | action="store_true", |
| 1068 | help="Include optional taxonomy databases such as GTDB in readiness checks.", |
| 1069 | ) |
| 1070 | parser.add_argument("--resource-checksums", action="store_true") |
| 1071 | parser.add_argument( |
| 1072 | "--require-resource-plan", |
| 1073 | action="store_true", |
| 1074 | help="Treat missing registered taxonomy/reference bundles as blocking for this direct runner.", |
| 1075 | ) |
| 1076 | parser.add_argument( |
| 1077 | "--skip-resource-plan", |
| 1078 | action="store_true", |
| 1079 | help="Skip registered taxonomy database readiness checks.", |
| 1080 | ) |
| 1081 | parser.add_argument("--outdir", type=Path) |
| 1082 | parser.add_argument("--run-id", default=slug_timestamp("amplicon-microbiome-backend")) |
| 1083 | parser.add_argument("--execute", action="store_true") |
| 1084 | return parser.parse_args() |
| 1085 | |
| 1086 | |
| 1087 | def serializable_args(args: argparse.Namespace) -> dict[str, Any]: |
no test coverage detected