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;
}
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;
}