Copy in external pre-called variants fed into analysis.

    Symlinks for non-CWL runs where we want to ensure VCF present
    in a local directory.

def _handle_precalled(data):
    """Copy in external pre-called variants fed into analysis.

    Symlinks for non-CWL runs where we want to ensure VCF present
    in a local directory.
    """
    if data.get("vrn_file") and not cwlutils.is_cwl_run(data):
        vrn_file = data["vrn_file"]
        if isinstance(vrn_file, (list, tuple)):
            assert len(vrn_file) == 1
            vrn_file = vrn_file[0]
        precalled_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "precalled"))
        ext = utils.splitext_plus(vrn_file)[-1]
        orig_file = os.path.abspath(vrn_file)
        our_vrn_file = os.path.join(precalled_dir, "%s-precalled%s" % (dd.get_sample_name(data), ext))
        utils.copy_plus(orig_file, our_vrn_file)
        data["vrn_file"] = our_vrn_file
    return data