Combine_Virulence_SignalP.smk 1.05 KB
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# Combine Virulence with SignalP
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import glob
import os

#################################
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# Combine Virulence and SignalP #
#################################
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rule merge_SignalPVir:
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    input:
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        hmm="{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_prediction.tsv",
        classifier="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}_classifier_results_formatted.tsv",
        SignalP="{datadir}/{project}/SignalP/aggregated/{sample}_SignalP_results.tsv",
        translation="{datadir}/{project}/renamed/{sample}_translation.tsv"
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    output:
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        Virulence_report="{datadir}/{project}/Virulence_prediction_{sample}_report.tsv"
    log:
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        "{datadir}/{project}/logs/{sample}.combine_virulence_results.log"
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    params:
        runtime=config["pathofact"]["runtime"]["short"],
        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
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    conda: "../../envs/R.yaml"
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    message: "Generate report on predicted virulence factors on the following sample(s): {wildcards.project} - {wildcards.sample}"
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    script: "../../scripts/Virulence.R"
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