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Add mash_db option to gtdb-tk #3

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Add mash_db option to gtdb-tk #3

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2 changes: 2 additions & 0 deletions config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -240,6 +240,8 @@ binning:
checkm: False
# run gtdbtk to classify bins phylogenetically?
gtdbtk: False
# run with mashdb as in latest versions of GTDB-TK
mash: False
# calculate average nucleotide identity for binned genomes with fastANI?
fastani: False

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5 changes: 3 additions & 2 deletions workflow/rules/binning.smk
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Expand Up @@ -514,7 +514,8 @@ rule gtdbtk_classify:
suff='fa',
indir=lambda wildcards, input: os.path.dirname(input.tsv),
dbdir=lambda wildcards, input: os.path.abspath(os.path.dirname(os.path.dirname(input.met))),
outdir=lambda wildcards, output: os.path.dirname(output[0])
outdir=lambda wildcards, output: os.path.dirname(output[0]),
mash="--mash_db resources/gtdb/mash" if "mash" in config["binning"].keys() and config["binning"]["mash"] else "",
threads: 20
resources:
runtime=lambda wildcards, attempt: attempt**2*60
Expand All @@ -530,7 +531,7 @@ rule gtdbtk_classify:
export GTDBTK_DATA_PATH={params.dbdir}
gtdbtk classify_wf -x {params.suff} --out_dir {params.outdir} \
--cpus {threads} --pplacer_cpus {threads} \
--genome_dir {params.indir} > {log} 2>&1
--genome_dir {params.indir} {params.mash} > {log} 2>&1
fi
"""

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