rule reorderSam:
    input:
        sam = __reorderSam__input
    params:
        genome = config['genome']['fasta_file']
    log:
        __reorderSam__logs
    output:
        __reorderSam__output
    shell:
        """
        ReorderSam I={input.sam} O={output} R={params.genome} CREATE_INDEX=true 2> {log}
        """