Metabinner Conda Workflow

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Requirements

Conda

Conda user guide

Code Snippets

shell:
    "(date && metaspades.py -k 21,33,55,77 -t {threads} -1 {input.read1} -2 {input.read2} -o $(dirname {output}) && date) 2> {log.err} > {log.out}"

SnakeMake metaspades From line 25 of rules/assembly.smk

shell:
    "(date && jgi_summarize_bam_contig_depths --outputDepth {output} {input} && "
    "date) 2> {log.err} > {log.out}"

SnakeMake From line 26 of rules/binning.smk

shell:
    "(date && metabat2 -i {input.contig} -a {input.cov} -o {output}/metabat -t {threads} && "
    "date) 2> {log.err} > {log.out}"

SnakeMake MetaBAT 2 From line 46 of rules/binning.smk

shell:
    "(date && cut_up_fasta.py {input.contig} -c 10000 -o 0 --merge_last -b {output.bed} > {output.cont} && "
    "concoct_coverage_table.py {output.bed} {input.bam} > {output.cov} && [[ -s {output.cov} ]] && "
    "date) 2> {log.err} > {log.out}"

SnakeMake CONCOCT From line 66 of rules/binning.smk

shell:
    "(date && concoct --composition_file {input.contig} --coverage_file {input.cov} -b $(dirname {output})/concoct -t {threads} && "
    "merge_cutup_clustering.py $(dirname {output})/concoct_clustering_gt1000.csv > {output} && "
    "date) 2> {log.err} > {log.out}"

SnakeMake CONCOCT From line 87 of rules/binning.smk

shell:
    "git clone https://github.com/ziyewang/MetaBinner.git &> /dev/null && "
    "mv MetaBinner $(dirname {output.dbs})"

SnakeMake From line 98 of rules/binning.smk

shell:
    """
    (date && jgi_summarize_bam_contig_depths --noIntraDepthVariance --outputDepth {output.temp} {input} && 
    cat {output.temp} | awk '{{if ($2>{config[metabinner][length]}) print $0 }}' | cut -f -1,4- > {output.final} && 
    date) 2> {log.err} > {log.out}
    """

SnakeMake From line 118 of rules/binning.smk

shell:
    "(date && python {input.bin}/scripts/Filter_tooshort.py {input.contig} {config[metabinner][length]} && "
    "python {input.bin}/scripts/gen_kmer.py {input.contig} {config[metabinner][length]} 4 && date) 2> {log.err} > {log.out}"

SnakeMake From line 189 of rules/binning.smk

shell:
    "(date && run_metabinner.sh -a {input.cont} -d {input.cov} -k {input.kmer} -p {input.path} -o $(dirname {output}) -t {threads} -s huge && "
    "mv $(dirname {output})/metabinner_res/* $(dirname {output}) && "
    "date) 2> {log.err} > {log.out}"

SnakeMake From line 211 of rules/binning.smk

shell:
    "(date && seqkit seq -j {threads} -o {output} -m 1499 {input} && date)"

SnakeMake seqkit From line 21 of rules/coverage.smk

shell:
    "(date && cat {input} > {output}  && date)"

SnakeMake From line 31 of rules/coverage.smk

shell:
    "(date && bwa index {input} && date) &> {log}"

SnakeMake BWA From line 47 of rules/coverage.smk

shell:
    "(date && bwa mem -t {threads} {input.cont} {input.read1} {input.read2} | samtools sort -@{threads} -o {output} - && " 
    "samtools index {output} && date) 2> {log.err} > {log.out}"