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busco.smk
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busco.smk
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rule dwld_busco_databases:
output:
directory('resources/busco_databases/metazoa_odb10'),
directory('resources/busco_databases/mollusca_odb10'),
params:
metazoa = config['busco']['metazoa'],
mollusca = config['busco']['mollusca'],
outdir = 'resources/busco_databases'
shell:
"""
cd {params.outdir}
wget -c {params.metazoa} -O - | tar -xz
wget -c {params.mollusca} -O - | tar -xz
"""
def get_busco_input(w):
if (w.version in ["GCA900618805", "GCA017311375", "GCA905397895", "GCA019925415"]):
return ancient(f"resources/{w.version}.fasta.gz")
else:
return ancient(f"results/fasta/{w.sample}_{w.version}.pseudohap.fasta.gz")
rule unzip_fasta:
input:
get_busco_input
output:
temp("results/fasta/{sample}_{version}.fa")
shell:
"zcat {input} > {output}"
rule busco:
input:
"results/fasta/{sample}_{version}.fa",
rules.dwld_busco_databases.output
output:
"results/busco/{sample}_{version}_{db}/run_{db}/short_summary.txt",
"results/busco/{sample}_{version}_{db}/short_summary.specific.{db}.{sample}_{version}_{db}.txt",
"results/busco/{sample}_{version}_{db}/run_{db}/full_table.tsv",
params:
db = lambda w: f'resources/busco_databases/{w.db}',
fa = lambda w, input: input[0].replace(".fasta.gz", ".fa"),
outdir = lambda w: f'{w.sample}_{w.version}_{w.db}'
wildcard_constraints:
db = '\w+_\w+'
log:
"logs/busco.{sample}_{version}_{db}.log"
threads:
config['busco']['threads']
conda:
"../envs/busco.yaml"
shell:
"""
busco -f -m genome -i {params.fa} -o {params.outdir} \
-q -c {threads} \
-l {params.db} > {log} 2>&1
cp -r {params.outdir} results/busco/ && rm -r {params.outdir}
"""
rule summarize_busco:
input:
expand("results/busco/{sample}_{version}_{db}/short_summary.specific.{db}.{sample}_{version}_{db}.txt",
sample=config['samples'],
version=["v1", "v2", "v3", "v4", "v5", "v6", "v7"],
db=["metazoa_odb10", "mollusca_odb10"]),
expand("results/busco/{pub}_{db}/short_summary.specific.{db}.{pub}_{db}.txt",
pub=['coruscus_GCA017311375', 'gallo_GCA900618805', 'edu_GCA905397895', 'eduam_GCA019925415'],
db=["metazoa_odb10", "mollusca_odb10"])
output:
"results/stats/busco_summary.tsv"
conda:
"../envs/busco.yaml"
shell:
"""
python workflow/scripts/summarize_buscos.py \
-o {output} \
--files {input}
"""