# include rules for the Analysis part of the workflow
include:
    '../rules/Universal/Preprocessing'
include:
    '../rules/Universal/SignalP'
include:
    '../rules/Virulence/Virulence'
include:
    '../rules/Virulence/Combine_Virulence_SignalP'
include:
    '../rules/Virulence/Virulence_report'
include:
    '../rules/Toxin/Toxin'
include:
    '../rules/Toxin/Combine_Toxin_SignalP'
include:
    '../rules/Toxin/Toxin_report'
include:
    '../rules/Universal/Preprocessing_contig'
include:
    '../rules/AMR/AMR'
include:
    '../rules/AMR/Plasmid'
include:
    '../rules/AMR/Phage'
include:
    '../rules/AMR/Combine_MGE_AMR'
include:
    '../rules/Universal/Combine_PathoFact'

# master command
rule Analysis:
    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"]
        )
    output:
        touch('PathoFact_analyis.done')