private TrimmomaticFields constructFieldsByIndex()

in src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java [102:131]
30 lines of code
6 McCabe index (conditional complexity)

    private TrimmomaticFields constructFieldsByIndex(Configuration configuration) {
        TrimmomaticFields trimmomaticFields = new TrimmomaticFields();
        if (index != null) {
            trimmomaticFields.index = String.valueOf(index);
        }
        trimmomaticFields.adapterSEQ = configuration.getGlobalConfig().getDatabaseConfig().getAdapterSEQ();
        trimmomaticFields.java = validate(configuration.getGlobalConfig().getToolConfig().getJava(),
                GlobalConfigFormat.JAVA);
        trimmomaticFields.numThreads = configuration.getGlobalConfig().getQueueParameters().getNumThreads();
        trimmomaticFields.trimmomatic = validate(configuration.getGlobalConfig().getToolConfig().getTrimmomatic(),
                GlobalConfigFormat.TRIMMOMATIC);
        trimmomaticFields.sfqOutdir = sample.getFastqOutdir();
        trimmomaticFields.sampleName = sample.getName();
        trimmomaticFields.fastq1 = result.getOut().getMergedFastq1();
        trimmomaticFields.fastq2 = result.getOut().getMergedFastq2();
        if (StringUtils.isNotBlank(trimmomaticFields.index)) {
            trimmomaticFields.prefix = format("%s/%s_%s", trimmomaticFields.sfqOutdir,
                    sample.getName(), trimmomaticFields.index);
        } else {
            trimmomaticFields.prefix = format("%s/%s", trimmomaticFields.sfqOutdir, sample.getName());
        }
        trimmomaticFields.trimmedFastq1 = format("%s.trimmed.R1.fastq.gz", trimmomaticFields.prefix);
        trimmomaticFields.trimmedFastq2 = StringUtils.isBlank(trimmomaticFields.fastq2) ? null
                : format("%s.trimmed.R2.fastq.gz", trimmomaticFields.prefix);
        trimmomaticFields.trimmedUnpairedFastq1 = StringUtils.isBlank(trimmomaticFields.fastq2) ? null
                : format("%s.trimmed_unpaired.R1.fq.gz", trimmomaticFields.prefix);
        trimmomaticFields.trimmedUnpairedFastq2 = StringUtils.isBlank(trimmomaticFields.fastq2) ? null
                : format("%s.trimmed_unpaired.R2.fq.gz", trimmomaticFields.prefix);
        return trimmomaticFields;
    }