Growth rate estimation

GRiD is implemented as follows:

rule grid:
    input:
        bins = f'{config["path"]["root"]}/{config["folder"]["reassembled"]}/{{IDs}}/reassembled_bins',
        R1 = rules.qfilter.output.R1, 
        R2 = rules.qfilter.output.R2
    output:
        directory(f'{config["path"]["root"]}/{config["folder"]["GRiD"]}/{{IDs}}')
    benchmark:
        f'{config["path"]["root"]}/benchmarks/{{IDs}}.grid.benchmark.txt'
    shell:
        """
        set +u;source activate {config[envs][metagem]};set -u
        cp -r {input.bins} {input.R1} {input.R2} $SCRATCHDIR
        cd $SCRATCHDIR
        cat *.gz > $(basename $(dirname {input.bins})).fastq.gz
        rm $(basename {input.R1}) $(basename {input.R2})
        mkdir MAGdb out
        update_database -d MAGdb -g $(basename {input.bins}) -p MAGdb
        rm -r $(basename {input.bins})
        grid multiplex -r . -e fastq.gz -d MAGdb -p -c 0.2 -o out -n {config[cores][grid]}
        rm $(basename $(dirname {input.bins})).fastq.gz
        mkdir {output}
        mv out/* {output}
        """