# Combine Virulence with SignalP

import glob
import os

#################################
# Combine Virulence and SignalP #
#################################

rule merge_SignalPVir:
    input:
        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"
    output:
        Virulence_report="{datadir}/{project}/Virulence_prediction_{sample}_report.tsv"
    log:
        "{datadir}/{project}/logs/{sample}.combine_virulence_results.log"
    params:
        runtime=config["pathofact"]["runtime"]["short"],
        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
    conda: "../../envs/R.yaml"
    message: "Generate report on predicted virulence factors on the following sample(s): {wildcards.project} - {wildcards.sample}"
    script: "../../scripts/Virulence.R"