Snakefile 1.9 KB
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#Snakefile
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configfile: "config.yaml"

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if config["workflow"] == "complete":
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    include:
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        "workflows/Combine_PathoFact_workflow.smk"
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    rule all:
        input:
            expand(
                [
                    "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv",
                    "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
                    "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
                ],
                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
            )
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elif config["workflow"] == "Tox":
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    include:
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        "workflows/Toxin_workflow.smk"
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    rule all:
        input:
            expand(
                [
                    "{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv",
                    "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv"
                ],
                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
            )
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elif config["workflow"] == "Vir":
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    include:
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        "workflows/Virulence_workflow.smk"
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    rule all:
        input:
            expand(
                "{OUTDIR}/{project}/Virulence_prediction_{input_file}_report.csv",
                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
            )                    
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elif config["workflow"] == "AMR":
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    include:
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        "workflows/AMR_workflow.smk"
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    rule all:
        input:
            expand(
                [
                    "{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv",
                    "{OUTDIR}/{project}/AMR/{input_file}_AMR_MGE_prediction_detailed.tsv"
                ],
                OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
            )
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else:
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    raise Exception("Unknown workflow option: %s" % config["workflow"])