rule tophat_mapping:
    """
    DEPRECATED rule for tophat mapper
    """


    input:
        fastq = __tophat_mapping__input,
        index = __tophat_mapping__prefix_done
    output:
        bam = __tophat_mapping__bam,
        sort = __tophat_mapping__sort
    log:
        __tophat_mapping__logs
    params:
        outdir = __tophat_mapping__outdir,
        prefix_index = __tophat_mapping__prefix,
        options = config["tophat_mapping"]["options"]
    threads:
        config["tophat_mapping"]["threads"]
    shell:
        """
        tophat --bowtie1 -p {threads} -o {params.outdir} {params.options} \
        {params.prefix_index} {input.fastq}  \
        && samtools sort -o {output.sort} {output.bam} 2> {log}
        """
