INNER CODE UNIT · Python

GTDBTK_DATA_PATH

franciscozorrilla/metaGEM · workflow/rules/Snakefile_single_end.smk.py:690

        export GTDBTK_DATA_PATH=/g/scb2/patil/zorrilla/conda/envs/gtdbtk/share/gtdbtk-1.1.0/db/

        cd $SCRATCHDIR
        cp -r {input} .

        gtdbtk classify_wf --genome_dir $(basename {input}) --out_dir GTDBtk -x fa --cpus {config[cores][gtdbtk]}
        mkdir -p {output}
        mv GTDBtk/* {output}

        """

rule classifyGenomes:
    input:
        bins = f'{config["path"]["root"]}/{config["folder"]["reassembled"]}/{{IDs}}/reassembled_bins',
        script = f'{config["path"]["root"]}/{config["folder"]["scripts"]}/classify-genomes'
    output:
        directory(f'{config["path"]["root"]}/{config["folder"]["classification"]}/{{IDs}}')
    benchmark:

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