protected JobOutput executeJellyfishMerger(
Args args, String ecqName, Set<File> fileSet, File outputDir)
throws InterruptedException, ProcessExecutionException, ConanParameterException, IOException {
String suffix = "jellyfish_" + ecqName + "_all.jf31_0";
String jobName = args.getJobPrefix() + "-merge-" + suffix;
List<File> files = new ArrayList<>();
files.addAll(fileSet);
File outputFile = new File(outputDir, suffix);
JellyfishMergeV11 jellyfishMerge =
this.makeJellyfishMerge(files, outputFile, args.getOrganism());
ExecutionResult id =
this.conanExecutorService.executeProcess(
jellyfishMerge,
args.getOutputDir(),
jobName,
args.getThreadsPerProcess(),
args.getMemoryPerProcess(),
args.isRunParallel());
id.setName("merge-" + suffix);
return new JobOutput(id, outputFile);
}
