# include rules for the Analysis part of the workflow
include:
    '../rules/Universal/Preprocessing'
include:
    '../rules/Universal/SignalP'
include:
    '../rules/Toxin/Toxin'
include:
    '../rules/Toxin/Combine_Toxin_SignalP'
include:
    '../rules/Toxin/Toxin_report'

# master command
rule Analysis:
    input:
        expand(
            [
                "{OUTDIR}/{project}/SignalP/aggregated/{input_file}_SignalP_results.txt",
                "{OUTDIR}/{project}/Toxin_gene_library_{input_file}_report.tsv",
                "{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv"
            ],
            OUTDIR=config["OUTDIR"], project=config["project"], input_file=config["input_file"]
        )
    output:
        touch('Toxin_analyis.done')