INNER CODE UNIT · Python

nSamples

franciscozorrilla/metaGEM · workflow/rules/Snakefile_single_end.smk.py:341

        nSamples=$(ls {input.READS}|wc -l)
        echo -e "\nDone mapping focal sample $fsampleID agains $nSamples samples in dataset folder."

        echo -e "\nRunning jgi_summarize_bam_contig_depths for all sorted bam files ... "
        jgi_summarize_bam_contig_depths --outputDepth $id.all.depth *.sort

        echo -e "\nRunning metabat2 ... "
        metabat2 -i $fsampleID.fa -a $id.all.depth -o $fsampleID

        mv *.fa $id.all.depth $(dirname {output})

        """


rule maxbin:
    input:
        assembly = rules.megahit.output,
        depth = rules.metabat.output

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