public static Flag buildFlags()

in src/main/java/com/epam/fonda/workflow/impl/Flag.java [68:110]

• 43 lines of code
• 1 McCabe index (conditional complexity)

    public static Flag buildFlags(final Configuration configuration) {
        final Set<String> tasks = configuration.getGlobalConfig().getPipelineInfo().getToolset();
        return Flag.builder()
                .rmdup(tasks.contains("rmdup"))
                .rsem(tasks.contains("rsem"))
                .rnaSeQC(tasks.contains("qc"))
                .xenome(configuration.getGlobalConfig().getPipelineInfo().isFlagXenome())
                .seqpurge(tasks.contains("seqpurge"))
                .trimmomatic(tasks.contains("trimmomatic"))
                .star(tasks.contains("star"))
                .hisat2(tasks.contains("hisat2"))
                .salmon(tasks.contains("salmon"))
                .featureCount(tasks.contains("featureCount"))
                .cufflinks(tasks.contains("cufflinks"))
                .stringtie(tasks.contains("stringtie"))
                .count(tasks.contains("count"))
                .doubletDetection(tasks.contains("doubletdetection"))
                .scrublet(tasks.contains("scrublet"))
                .conversion(tasks.contains("conversion"))
                .qc(tasks.contains("qc"))
                .vdj(tasks.contains("vdj"))
                .vardict(tasks.contains("vardict"))
                .mutect1(tasks.contains("mutect1"))
                .mutect2(tasks.contains("mutect2"))
                .lofreq(tasks.contains("lofreq"))
                .gatkHaplotypeCaller(tasks.contains("gatkHaplotypeCaller"))
                .strelka2(tasks.contains("strelka2"))
                .scalpel(tasks.contains("scalpel"))
                .starFusion(tasks.contains("starFusion"))
                .fusionCatcher(tasks.contains("fusionCatcher"))
                .sequenza(tasks.contains("sequenza"))
                .exomecnv(tasks.contains("exomecnv"))
                .freebayes(tasks.contains("freebayes"))
                .bwa(tasks.contains("bwa"))
                .novoalign(tasks.contains("novoalign"))
                .picard(tasks.contains("picard"))
                .abraRealign(tasks.contains("abra_realign"))
                .gatkRealign(tasks.contains("gatk_realign"))
                .contEst(tasks.contains("contEst"))
                .mixcr(tasks.contains("mixcr"))
                .optiType(tasks.contains("optitype"))
                .build();
    }