Run Scalpel indel calling, either paired tumor/normal or germline calling.

def run_scalpel(align_bams, items, ref_file, assoc_files, region=None,
                  out_file=None):
    """Run Scalpel indel calling, either paired tumor/normal or germline calling.
    """
    if region is None:
        message = ("A region must be provided for Scalpel")
        raise ValueError(message)
    if is_paired_analysis(align_bams, items):
        call_file = _run_scalpel_paired(align_bams, items, ref_file,
                                          assoc_files, region, out_file)
    else:
        call_file = _run_scalpel_caller(align_bams, items, ref_file,
                                          assoc_files, region, out_file)
    return call_file