Combine_MGE_AMR.smk 1.31 KB
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#AMR

import glob
import os

##########################
#     AMR Prediction     #
##########################

rule combine_AMR_plasmid:
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    input:
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        ORF_translation="{datadir}/{project}/renamed/{sample}_translation.tsv",
        Contig_ORFs="{datadir}/{project}/Prodigal/{sample}.contig",
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        Contig_translation="{datadir}/{project}/renamed/{sample}_Contig_translation.tsv",
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        AMR="{datadir}/{project}/AMR/{sample}_AMR_prediction.tsv",
        PlasFlow="{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_prediction_final.tsv",
        MOB_suite="{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}_MOB_suite_aggregated.tsv",
        DeepVirFinder="{datadir}/{project}/MGE/phage/{sample}_VirFinder_aggregated.csv",
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        VirSorter="{datadir}/{project}/MGE/phage/{sample}_VIRSorter_aggregated.csv"
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    output:    
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        Report_1="{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv",
        Report_2="{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv"
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    log:
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        "{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_detail_temp.log"
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    params:
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        outdir="{datadir}",
        runtime=config["pathofact"]["runtime"]["medium"],
        mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
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    conda:
        "../../envs/R.yaml"
    script:
        "../../scripts/AMR_MGE.R"
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