from sequana_wrappers import get_shell

rule all:
    input:
        multiext("reference/genome", ".1.bt2", ".2.bt2", ".3.bt2", ".4.bt2", ".rev.1.bt2", ".rev.2.bt2")

rule bowtie2_build:
    input:
        reference="reference/genome.fasta"
    output:
        multiext("reference/genome", ".1.bt2", ".2.bt2", ".3.bt2", ".4.bt2", ".rev.1.bt2", ".rev.2.bt2")
    log:
        "logs/bowtie2_build.log"
    params:
        options=""
    threads: 2
    container:
        "https://zenodo.org/record/8092297/files/bowtie2_2.5.1.img"
    shell:
        get_shell("bowtie2/build", "v1")
