public void run()

in src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java [57:82]

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

    public void run(Configuration configuration, FastqFileSample sample) throws IOException {
        configuration.setCustTask("alignment");
        BamResult bamResult;
        if ("VDJ".equalsIgnoreCase(sample.getSampleType())) {
            if (!flag.isVdj()) {
                return;
            }
            bamResult = new Vdj(sample, BamResult.builder()
                    .bamOutput(BamOutput.builder().build())
                    .command(BashCommand.withTool("")).build())
                    .generate(configuration, TEMPLATE_ENGINE);
        } else {
            bamResult = new Alignment().estimating(flag, sample, configuration, TEMPLATE_ENGINE);
        }
        final String toolCommand = bamResult.getCommand().getToolCommand();
        final String cmd = configuration.isMasterMode()
                ? toolCommand
                : toolCommand + cleanUpTmpDir(bamResult.getCommand().getTempDirs());

        final String custScript = printShell(configuration, cmd, sample.getName(), null);
        if (scriptManager != null) {
            scriptManager.addScript(sample.getName(), ALIGNMENT, custScript);
            bamResult.getCommand().getTempDirs().forEach(t -> scriptManager.addScript(sample.getName(), TEMP, t));
        }
        log.debug(String.format("Successful Step: the %s sample was processed.", sample.getName()));
    }