Example #1
0
    public RampartProcessArgs(RampartStage stage) {

      super(new Params());

      this.outputDir = new File("");
      this.samples = new ArrayList<>();
      this.threads = DEFAULT_THREADS;
      this.memoryMb = DEFAULT_MEMORY;
      this.runParallel = DEFAULT_RUN_PARALLEL;
      this.stage = stage;
      this.organism = null;

      Format formatter = new SimpleDateFormat("yyyyMMdd_HHmmss");
      String dateTime = formatter.format(new Date());
      this.jobPrefix = "rampart-" + stage.getOutputDirName() + "-" + dateTime;
    }
Example #2
0
    public RampartProcessArgs(
        RampartStage stage,
        File outputDir,
        String jobPrefix,
        List<Mecq.Sample> samples,
        Organism organism,
        boolean runParallel)
        throws IOException {

      // Set defaults first
      this(stage);

      // Set from parameters
      this.outputDir = outputDir;
      this.jobPrefix = jobPrefix + "-" + stage.getOutputDirName();
      this.samples = samples;
      this.organism = organism;
      this.runParallel = runParallel;
    }