public FastqResult process()

in src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java [55:66]

• 12 lines of code
• 5 McCabe index (conditional complexity)

    public FastqResult process(final Flag flag, final FastqFileSample sample, final Configuration configuration,
                               final TemplateEngine templateEngine) {
        if (flag.isXenome()) {
            fastqResult = new Xenome(sample, fastqResult, index).generate(configuration, templateEngine);
        }
        if (flag.isSeqpurge() && !skipTool(configuration)) {
            fastqResult = new SeqPurge(sample, fastqResult, index).generate(configuration, templateEngine);
        } else if (flag.isTrimmomatic()) {
            fastqResult = new Trimmomatic(sample, fastqResult, index).generate(configuration, templateEngine);
        }
        return fastqResult;
    }