intial version

workflow/rules/preparation.smk

@@ -0,0 +1,84 @@
+import os
+import hashlib
+
+# Prepwork
+
+def get_genome_file_name(wildcards):
+    return '../data/reference_genomes/'+'_'.join(x.lower() for x in wildcards.species.split())+'.fasta'
+
+def get_unique_download_dir(wildcards):
+    unique_id = hashlib.md5(wildcards.species.encode()).hexdigest()[:8]
+    return config["tmp_dir"]+'/'+unique_id
+
+def format_cli_arg(wildcards):
+    # Replaces underscores with spaces for the CLI command
+    return wildcards.species.replace("_", " ")
+
+rule pull_ncbi_datasets_cli:
+    output:
+        config["datasets_binary"]
+    params:
+        arch=config["arch"]
+    threads: 1
+    shell:
+        """
+        curl https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-{params.arch}/datasets -o {output}
+        chmod a+x {output}
+        """
+
+rule pull_dorado_models:
+    output:
+        directory(f"{config['dorado_model_dir']}/{config['fast_model_name']}"),
+        directory(f"{config['dorado_model_dir']}/{config['hac_model_name']}")
+    threads: 1
+    shell:
+        """
+        dorado download --models-directory {config[dorado_model_dir]} --model {config[fast_model_name]}
+        dorado download --models-directory {config[dorado_model_dir]} --model {config[hac_model_name]}
+        """
+
+rule download_reference_genome:
+    input:
+        config["datasets_binary"]
+    output:
+        temp('../data/reference_genomes/{species}.fasta')
+    params:
+        api_key=os.environ['NCBI_API_KEY'],
+        wd=get_unique_download_dir,
+        ncbi_tax_name=lambda w: format_cli_arg(w)
+    threads: 1
+    shell:
+        """
+        echo {wildcards.species}
+        rm -rf {params.wd}
+        mkdir {params.wd}
+        {config[datasets_binary]} download genome taxon "{params.ncbi_tax_name}" --reference --no-progressbar --filename {params.wd}/{wildcards.species}.zip
+        unzip -d {params.wd} -o {params.wd}/{wildcards.species}.zip 
+        mv {params.wd}/ncbi_dataset/data/*/*fna {output}
+        rm -rf {params.wd}
+        """
+
+rule concatenate_reference_genomes:
+    input:
+        expand("../data/reference_genomes/{species}.fasta",species=config["species_list"])
+    output:
+        "../data/reference_genomes/full_reference.fasta"
+    threads: 1
+    shell:
+        """
+        cat {input} > {output}
+        """
+
+rule create_minimap_index:
+    input: 
+        "../data/reference_genomes/full_reference.fasta"
+    output:
+        "../data/reference_genomes/full_reference.mmi"
+    threads:
+        32
+    conda:
+        "../envs/minimap.yaml"
+    shell:
+        """
+        minimap2 -x map-ont -t {threads} -d {output} {input}
+        """