Snakefile

configfile: "config/config_dengue.yaml"

serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4']
genes = ['genome']

wildcard_constraints:
    serotype = "|".join(serotypes),
    gene = "|".join(genes)

rule all:
    input:
        auspice_json = expand("auspice/dengue_{serotype}_{gene}.json", serotype=serotypes, gene=genes),
        nextclade_dataset = expand("datasets/{serotype}/tree.json", serotype=serotypes),
        test_dataset = expand("test_output/{serotype}", serotype=serotypes),

include: "rules/prepare_sequences.smk"
include: "rules/construct_phylogeny.smk"
include: "rules/annotate_phylogeny.smk"
include: "rules/export.smk"
include: "rules/assemble_dataset.smk"

# Include custom rules defined in the config.
if "custom_rules" in config:
    for rule_file in config["custom_rules"]:

        include: rule_file

rule clean:
    """Removing directories: {params}"""
    params:
        "results ",
        "auspice"
    shell:
        "rm -rfv {params}"