rule all:
    input: "test/sequana_coverage.html", "test2/sequana_coverage.html"

# on purpose, we do not provide low/high in the params section to test the
# wrapper ability to set default values


rule sequana_coverage_with_gbk:
    input:
        bed = "test.bed",
        fasta = "measles.fa",
        gbk = "measles.gbk"
    output:
        html = "test/sequana_coverage.html"
    params:
        chunksize = 5000000,
        circular = True,
        double_threshold = 0.5,
        gc_window_size = 201,
        mixture_models = 2,
        window_size = 3001,
        high_threshold=2
    wrapper:
        "main/wrappers/sequana_coverage"


rule sequana_coverage:
    input:
        bed = "test.bed",
        fasta = "measles.fa",
    output:
        html = "test2/sequana_coverage.html"
    params:
        circular = True,
        chunksize = 5000000,
        double_threshold = 0.5,
        gc_window_size = 201,
        mixture_models = 2,
        window_size = 3001,
        high_threshold=2
    wrapper:
        "main/wrappers/sequana_coverage"
