Retrieve a list of QC tools to use based on configuration and analysis type.

    Uses defaults if previously set.

def get_qc_tools(data):
    """Retrieve a list of QC tools to use based on configuration and analysis type.

    Uses defaults if previously set.
    """
    if dd.get_algorithm_qc(data):
        return dd.get_algorithm_qc(data)
    analysis = data["analysis"].lower()
    to_run = []
    if tz.get_in(["config", "algorithm", "kraken"], data):
        to_run.append("kraken")
    if "fastqc" not in dd.get_tools_off(data):
        to_run.append("fastqc")
    if any([tool in dd.get_tools_on(data)
            for tool in ["qualimap", "qualimap_full"]]):
        to_run.append("qualimap")
    if analysis.startswith("rna-seq") or analysis == "smallrna-seq":
        if "qualimap" not in dd.get_tools_off(data):
            if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):
                to_run.append("qualimap_rnaseq")
            else:
                logger.debug("GTF not compatible with Qualimap, skipping.")
    if analysis.startswith("chip-seq"):
        to_run.append("chipqc")
    if analysis.startswith("smallrna-seq"):
        to_run.append("small-rna")
        to_run.append("atropos")
    if "coverage_qc" not in dd.get_tools_off(data):
        to_run.append("samtools")
    if dd.has_variantcalls(data):
        if "coverage_qc" not in dd.get_tools_off(data):
            to_run += ["coverage", "picard"]
        to_run += ["qsignature", "variants"]
        if vcfanno.is_human(data):
            to_run += ["contamination", "peddy"]
        if vcfutils.get_paired_phenotype(data):
            to_run += ["viral"]
        if damage.should_filter([data]):
            to_run += ["damage"]
    if dd.get_umi_consensus(data):
        to_run += ["umi"]
    if tz.get_in(["config", "algorithm", "preseq"], data):
        to_run.append("preseq")
    to_run = [tool for tool in to_run if tool not in dd.get_tools_off(data)]
    to_run.sort()
    return to_run