Perform detection of structural variations with Manta.

def run(items):
    """Perform detection of structural variations with Manta.
    """
    paired = vcfutils.get_paired(items)
    data = paired.tumor_data if paired else items[0]
    work_dir = _sv_workdir(data)
    variant_file = _get_out_file(work_dir, paired)
    if not utils.file_exists(variant_file):
        with file_transaction(data, work_dir) as tx_work_dir:
            utils.safe_makedir(tx_work_dir)
            tx_workflow_file = _prep_config(items, paired, tx_work_dir)
            _run_workflow(items, paired, tx_workflow_file, tx_work_dir)
    assert utils.file_exists(variant_file), "Manta finished without output file %s" % variant_file
    variant_file = shared.annotate_with_depth(variant_file, items)
    out = []
    upload_counts = collections.defaultdict(int)
    for data in items:
        if "break-point-inspector" in dd.get_tools_on(data):
            if paired and paired.normal_bam and paired.tumor_name == dd.get_sample_name(data):
                variant_file = _run_break_point_inspector(data, variant_file, paired, work_dir)
        if "sv" not in data:
            data["sv"] = []
        final_vcf = shared.finalize_sv(variant_file, data, items)
        vc = {"variantcaller": "manta",
              "do_upload": upload_counts[final_vcf] == 0,  # only upload a single file per batch
              "vrn_file": final_vcf}
        evidence_bam = _get_evidence_bam(work_dir, data)
        if evidence_bam:
            vc["read_evidence"] = evidence_bam
        data["sv"].append(vc)
        upload_counts[final_vcf] += 1
        out.append(data)
    return out