Prepare data to run alignment step, only once for each project

def run_align(*data):
    """
    Prepare data to run alignment step, only once for each project
    """
    work_dir = dd.get_work_dir(data[0][0])
    out_dir = op.join(work_dir, "seqcluster", "prepare")
    seq_out = op.join(out_dir, "seqs.fastq")
    bam_dir = op.join(work_dir, "align")
    new_bam_file = op.join(bam_dir, "seqs.bam")
    tools = dd.get_expression_caller(data[0][0])
    if not file_exists(new_bam_file):
        sample = process_alignment(data[0][0], [seq_out, None])
        bam_file = dd.get_work_bam(sample[0][0])
        shutil.move(bam_file, new_bam_file)
        shutil.move(bam_file + ".bai", new_bam_file + ".bai")
        shutil.rmtree(op.join(bam_dir, sample[0][0]["rgnames"]['sample']))
    for sample in data:
        # sample[0]["align_bam"] = sample[0]["clean_fastq"]
        sample[0]["cluster_bam"] = new_bam_file

    if "mirdeep2" in tools:
        novel_db = mirdeep.run(data)
    return data