(args: argparse.Namespace)
| 274 | |
| 275 | |
| 276 | def build_nfcore_plan(args: argparse.Namespace) -> list[dict[str, Any]]: |
| 277 | cmd = [ |
| 278 | "python", |
| 279 | "plugins/ngs-analysis/scripts/run_nfcore_pipeline.py", |
| 280 | "--pipeline", |
| 281 | "ampliseq", |
| 282 | "--sample-sheet", |
| 283 | args.sample_sheet.expanduser().resolve(), |
| 284 | "--extra-param", |
| 285 | f"FW_primer={args.primer_forward}", |
| 286 | "--extra-param", |
| 287 | f"RV_primer={args.primer_reverse}", |
| 288 | ] |
| 289 | if args.profile: |
| 290 | cmd.extend(["--profile", args.profile]) |
| 291 | if args.execute: |
| 292 | cmd.append("--execute") |
| 293 | return [command_plan_entry("nf-core/ampliseq handoff", cmd, outputs=["nfcore/ampliseq"])] |
| 294 | |
| 295 | |
| 296 | def build_plan(args: argparse.Namespace, samples: list[dict[str, str]]) -> list[dict[str, Any]]: |
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