public String generate()

in src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java [79:101]

• 21 lines of code
• 6 McCabe index (conditional complexity)

    public String generate(Configuration configuration, TemplateEngine templateEngine) {
        if (!checkToolset(flag) || isWgsWorkflow(configuration)) {
            return StringUtils.EMPTY;
        }

        if (CollectionUtils.isEmpty(fastqSamples) && CollectionUtils.isEmpty(bamSamples)) {
            throw new IllegalArgumentException(
                    "Error: no sample files are properly provided, please check!");
        }

        final StringBuilder cmd = new StringBuilder();
        filterToolset(flag)
                .forEach(tool -> periodicDnaMutationStatusCheck(configuration, templateEngine, cmd, tool));
        final String mutationAnalysis = RnaAnalysisUtils.dnaRnaMutationAnalysis(configuration, templateEngine,
                String.join("+", configuration.getGlobalConfig().getPipelineInfo().getToolset()));
        cmd.append(mutationAnalysis);
        configuration.setCustTask("mergeMutation");
        try {
            return PipelineUtils.printShell(configuration, cmd.toString(), null, null);
        } catch (IOException e) {
            throw new IllegalArgumentException("Cannot create bash script for DNA analysis post processing");
        }
    }