CWL target to skip alignment and organize input data.

def organize_noalign(data):
    """CWL target to skip alignment and organize input data.
    """
    data = utils.to_single_data(data[0])
    work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data)))
    work_bam = os.path.join(work_dir, "%s-input.bam" % dd.get_sample_name(data))
    if data.get("files"):
        if data["files"][0].endswith(".cram"):
            work_bam = cram.to_bam(data["files"][0], work_bam, data)
        else:
            assert data["files"][0].endswith(".bam"), data["files"][0]
            utils.copy_plus(data["files"][0], work_bam)
        bam.index(work_bam, data["config"])
    else:
        work_bam = None
    data["align_bam"] = work_bam
    return data