rule samtools__prepare_fai_index:
    """
    Index fasta file to quicker retrieve substring sequences
    :input reference: Genomic sequence file in fasta format to index
    :output dict: Index for the input reference genomic file
    """
    input:
        reference = '{genome}.fa'
    output:
        '{genome}.fa.fai'
    conda:
        config['snakelines_dir'] + '/enviroments/samtools.yaml'
    shell:
        """
        samtools faidx {input.reference}
        """