from sequana_wrappers import get_shell

rule all:
    input: ["genome.fasta.bwt", "genome.fasta.fai"]

rule bwa_build:
    input:
        reference="genome.fasta"
    output:
        bwa_bwt="genome.fasta.bwt",
        fai="genome.fasta.fai"
    log:
        "logs/bwa_build.log"
    params:
        options="",
        index_algorithm="is"
    threads: 2
    container:
        "https://zenodo.org/record/7341710/files/sequana_tools_0.14.5.img"
    shell:
        get_shell("bwa/build", "v1")
