public Workflow getWorkflow()

in src/main/java/com/epam/fonda/workflow/WorkflowFactory.java [43:73]

• 31 lines of code
• 18 McCabe index (conditional complexity)

    public Workflow getWorkflow(final String workflowName, final Configuration configuration) {
        final Flag flag = Flag.buildFlags(configuration);
        final ScriptManager scriptManager = configuration.isMasterMode()
                ? MasterScript.getInstance()
                : null;
        switch (PipelineType.getByName(workflowName)) {
            case RNA_EXPRESSION_FASTQ:
            case SC_RNA_EXPRESSION_FASTQ:
            case RNA_CAPTURE_VAR_FASTQ:
                return new RnaExpressionFastqWorkflow(flag, scriptManager);
            case SC_RNA_EXPRESSION_CELLRANGER_FASTQ:
                return new SCRnaExpressionCellRangerFastqWorkflow(flag, scriptManager);
            case RNA_EXPRESSION_BAM:
            case SC_RNA_EXPRESSION_BAM:
                return new RnaExpressionBamWorkflow(flag, scriptManager);
            case RNA_FUSION_FASTQ: return new RnaFusionFastqWorkflow(flag, scriptManager);
            case DNA_AMPLICON_VAR_FASTQ: return new DnaVarFastqWorkflow(flag, "Index mkdup bam", scriptManager);
            case DNA_CAPTURE_VAR_FASTQ:
            case DNA_WGS_VAR_FASTQ:
                return new DnaVarFastqWorkflow(flag, "Index rmdup bam", scriptManager);
            case DNA_AMPLICON_VAR_BAM:
            case DNA_CAPTURE_VAR_BAM:
            case DNA_WGS_VAR_BAM:
                return new DnaVarBamWorkflow(flag, scriptManager);
            case BAM_2_FASTQ: return new Bam2FastqWorkflow(flag, scriptManager);
            case TCR_REPERTOIRE_FASTQ: return new TcrRepertoireFastqWorkflow(flag, scriptManager);
            case HLA_TYPING_FASTQ: return new HlaTypingFastqWorkflow(flag, scriptManager);
            default: throw new IllegalArgumentException(String.format("Requested workflow %s is not supported yet",
                    workflowName));
        }
    }