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standage
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May 1, 2025
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| def run_snakemake(config, workdir, cores=1, dryrun=False): | ||
| outcfg = smk_types.OutputSettings(printshellcmds=True) | ||
| with smk_api(outcfg) as smk: | ||
| workflow = smk.workflow( | ||
| config_settings=smk_types.ConfigSettings(config=config), | ||
| storage_settings=smk_types.StorageSettings(), | ||
| resource_settings=smk_types.ResourceSettings(cores=cores), | ||
| snakefile=files("microhapulator") / "workflows" / "analysis.smk", | ||
| workdir=Path(workdir), | ||
| ) | ||
| dag = workflow.dag(smk_types.DAGSettings(targets=["report"])) | ||
| mode = "dryrun" if dryrun else "local" | ||
| dag.execute_workflow(executor=mode) |
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This is close to the minimal code required to replicate the flags I commonly used with the snakemake.snakemake command in version 7 and below.
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| "analysis/{}/03typing/callplots".format(wildcards.sample), | ||
| f"analysis/{wildcards.sample}/03typing/callplots", |
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Reinstating f-strings since they don't break Python 3.12 in Snakemake 9.
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| threshfile="" if config["thresh_file"] == "" else f"--config {config['thresh_file']}", | ||
| threshfile=( | ||
| "" if config["thresh_file"] in ("", None) else f"--config {config['thresh_file']}" | ||
| ), |
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I think the newer versions of Snakemake were converting the empty string in the config dictionary into None, so this change just accounts for both.
| outfile = Path(outfile) | ||
| # Snakemake f-strings break with Python 3.12: https://github.com/snakemake/snakemake/issues/2648 | ||
| linkfile = "{}/R{}-fastqc.html".format(params.outdir, end) | ||
| linkfile = f"{params.outdir}/R{end}-fastqc.html" |
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Another reinstated f-string.
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| mhrefr=str(Path(args.markerrefr).resolve()), | ||
| mhdefn=str(Path(args.markerdefn).resolve()), | ||
| hg38path=str(Path(args.hg38).resolve()), | ||
| hg38index=str(Path(args.hg38idx).resolve()), |
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Passing paths here also caused an issue with newer versions of Snakemake where they didn't with version 7. 🤷♂️
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This PR implements support for Snakemake version 8.