# include rules for the Analysis part of the workflow
include:
    '../rules/Universal/Preprocessing'
include:
    '../rules/Universal/Preprocessing_contig'
include:
    '../rules/AMR/AMR'
include:
    '../rules/AMR/Plasmid'
include:
    '../rules/AMR/Phage'
include:
    '../rules/AMR/Combine_MGE_AMR'

# master command
rule AMR_Analysis:
    input: 
        expand(
            [
                "{OUTDIR}/{project}/MGE/phage/{input_file}_VIRSorter_aggregated.csv",
                "{OUTDIR}/{project}/MGE/phage/{input_file}_VirFinder_aggregated.csv",
                "{OUTDIR}/{project}/MGE/plasmid/{input_file}_plasflow_prediction_final.tsv", 
                "{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"]
        )
    output:
        touch('AMR_analyis.done')