Snakefile

include: "common.smk"


pepfile: config["pepfile"]


rule all:
    input:
        outfile=get_outfile(),
        samples=expand("{sample}.txt", sample=pep.sample_table["sample_name"]),
        bams=expand("{sample}.bam", sample=pep.sample_table["sample_name"]),
        settings="settings.txt",


rule example:
    output:
        get_outfile(),
    log:
        "log/stdout.txt",
    container:
        containers["debian"]
    shell:
        """
        echo "Hello world!" > {output} 2> {log}
        """


rule sample:
    output:
        "{sample}.txt",
    log:
        "log/{sample}_touch.txt",
    container:
        containers["debian"]
    shell:
        """
        touch {output} 2> {log}
        """


rule map:
    input:
        f=get_forward,
        r=get_reverse,
    output:
        "{sample}.bam",
    log:
        "log/{sample}_map.txt",
    container:
        containers["debian"]
    shell:
        """
        echo mem ref.fa {input.f} {input.r} > {output}
        """


rule settings:
    output:
        "settings.txt",
    params:
        s1=config["setting1"],
        s2=config["setting2"],
        s3=config["setting3"],
    log:
        "log/settings.txt",
    container:
        containers["debian"]
    shell:
        """
        echo {params.s1} {params.s2} {params.s3} > {output}
        """