Snakefile

configfile: "config/configfile.yaml"


wildcard_constraints:
    a_or_b=r"a|b",


build_dir = "results"
auspice_dir = "auspice"


rule all:
    input:
        expand(
            "auspice/rsv_{subtype}_{build}_{resolution}.json",
            subtype=config.get("subtypes", ["a"]),
            build=config.get("builds_to_run", ["genome"]),
            resolution=config.get("resolutions_to_run", ["all-time"]),
        ),


include: "workflow/snakemake_rules/chores.smk"
include: "workflow/snakemake_rules/core.smk"
include: "workflow/snakemake_rules/export.smk"
include: "workflow/snakemake_rules/download.smk"
include: "workflow/snakemake_rules/merge.smk"
include: "workflow/snakemake_rules/glycosylation.smk"
include: "workflow/snakemake_rules/clades.smk"


if "deploy_url" in config:

    include: "workflow/snakemake_rules/nextstrain_automation.smk"


rule clean:
    params:
        targets=["auspice", "results"],
    shell:
        """
        rm -rf {params.targets}
        """


rule clobber:
    params:
        targets=["data", "auspice", "results"],
    shell:
        """
        rm -rf {params.targets}
        """