85 lines
2.5 KiB
Plaintext
85 lines
2.5 KiB
Plaintext
import os
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import hashlib
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# Prepwork
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def get_genome_file_name(wildcards):
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return '../data/reference_genomes/'+'_'.join(x.lower() for x in wildcards.species.split())+'.fasta'
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def get_unique_download_dir(wildcards):
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unique_id = hashlib.md5(wildcards.species.encode()).hexdigest()[:8]
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return config["tmp_dir"]+'/'+unique_id
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def format_cli_arg(wildcards):
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# Replaces underscores with spaces for the CLI command
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return wildcards.species.replace("_", " ")
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rule pull_ncbi_datasets_cli:
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output:
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config["datasets_binary"]
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params:
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arch=config["arch"]
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threads: 1
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shell:
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"""
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curl https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-{params.arch}/datasets -o {output}
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chmod a+x {output}
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"""
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rule pull_dorado_models:
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output:
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directory(f"{config['dorado_model_dir']}/{config['fast_model_name']}"),
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directory(f"{config['dorado_model_dir']}/{config['hac_model_name']}")
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threads: 1
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shell:
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"""
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dorado download --models-directory {config[dorado_model_dir]} --model {config[fast_model_name]}
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dorado download --models-directory {config[dorado_model_dir]} --model {config[hac_model_name]}
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"""
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rule download_reference_genome:
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input:
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config["datasets_binary"]
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output:
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temp('../data/reference_genomes/{species}.fasta')
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params:
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api_key=os.environ['NCBI_API_KEY'],
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wd=get_unique_download_dir,
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ncbi_tax_name=lambda w: format_cli_arg(w)
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threads: 1
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shell:
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"""
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echo {wildcards.species}
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rm -rf {params.wd}
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mkdir {params.wd}
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{config[datasets_binary]} download genome taxon "{params.ncbi_tax_name}" --reference --no-progressbar --filename {params.wd}/{wildcards.species}.zip
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unzip -d {params.wd} -o {params.wd}/{wildcards.species}.zip
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mv {params.wd}/ncbi_dataset/data/*/*fna {output}
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rm -rf {params.wd}
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"""
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rule concatenate_reference_genomes:
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input:
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expand("../data/reference_genomes/{species}.fasta",species=config["species_list"])
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output:
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"../data/reference_genomes/full_reference.fasta"
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threads: 1
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shell:
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"""
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cat {input} > {output}
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"""
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rule create_minimap_index:
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input:
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"../data/reference_genomes/full_reference.fasta"
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output:
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"../data/reference_genomes/full_reference.mmi"
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threads:
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32
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conda:
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"../envs/minimap.yaml"
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shell:
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"""
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minimap2 -x map-ont -t {threads} -d {output} {input}
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"""
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