CWL entry point: combine variant calls from regions into single VCF.

def concat_batch_variantcalls(items, region_block=True, skip_jointcheck=False):
    """CWL entry point: combine variant calls from regions into single VCF.
    """
    items = [utils.to_single_data(x) for x in items]
    batch_name = _get_batch_name(items, skip_jointcheck)
    variantcaller = _get_batch_variantcaller(items)
    # Pre-called input variant files
    if not variantcaller and all(d.get("vrn_file") for d in items):
        return {"vrn_file": items[0]["vrn_file"]}
    out_file = os.path.join(dd.get_work_dir(items[0]), variantcaller, "%s.vcf.gz" % (batch_name))
    utils.safe_makedir(os.path.dirname(out_file))
    if region_block:
        regions = [_region_to_coords(rs[0]) for rs in items[0]["region_block"]]
    else:
        regions = [_region_to_coords(r) for r in items[0]["region"]]
    vrn_file_regions = items[0]["vrn_file_region"]
    out_file = vcfutils.concat_variant_files(vrn_file_regions, out_file, regions,
                                             dd.get_ref_file(items[0]), items[0]["config"])
    return {"vrn_file": out_file}