rule bwa_index:
    input:
        reference="genome.fasta"
    output:
        "genome.fasta.bwt",
        "genome.fasta.fai"
    log:
        "logs/bwa_build/build.log"
    params:
        options="",
        index_algorithm="is"
        # 'is' for short genome and bwtsw' for long genomes. No information form bwa about what is long or short
    wrapper:
        "main/wrappers/bwa/build"
