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private void myMethod () {LocalDateTime l =
new LocalDateTime()
- Smart code suggestions by Codota
}
public static CondorJob createJob(int count, Class<?> moduleClass, WorkflowPlan workflowPlan, HTSFSample htsfSample) { return createJob(count, moduleClass, workflowPlan, htsfSample, true); }
public static CondorJob createJob(int count, Class<?> moduleClass, WorkflowPlan workflowPlan, HTSFSample htsfSample, boolean persistFileData) { return createJob(count, moduleClass, workflowPlan, htsfSample, persistFileData, 3); }
public static CondorJob createJob(int count, Class<?> moduleClass, WorkflowPlan workflowPlan) { return createJob(count, moduleClass, workflowPlan, null); }
CondorJob randomSampleFastqJob = PipelineJobFactory.createJob(++count, RandomSampleFastqCLI.class, getWorkflowPlan(), htsfSample); randomSampleFastqJob.addArgument(RandomSampleFastqCLI.FASTQ, trimmedFastq.getAbsolutePath()); CondorJob bwaAlignJob = PipelineJobFactory.createJob(++count, BWAAlignCLI.class, getWorkflowPlan(), htsfSample); bwaAlignJob.setNumberOfProcessors(8); CondorJob bwaSAMSingleEndJob = PipelineJobFactory.createJob(++count, BWASAMSingleEndCLI.class, getWorkflowPlan(), htsfSample); bwaSAMSingleEndJob.addArgument(BWASAMSingleEndCLI.FASTADB, sequenceFastaDB); CondorJob genomeSampleQCJob = PipelineJobFactory.createJob(++count, GenomeSampleQCCLI.class, getWorkflowPlan(), htsfSample); genomeSampleQCJob.addArgument(GenomeSampleQCCLI.KEY, key); CondorJob rnaSampleQCJob = PipelineJobFactory.createJob(++count, RNASampleQCCLI.class, getWorkflowPlan(), htsfSample); rnaSampleQCJob.addArgument(RNASampleQCCLI.KEY, key);
CondorJob fastxQualityStatsJob = PipelineJobFactory.createJob(++count, FastxQualityStatsCLI.class, getWorkflowPlan(), htsfSample); fastxQualityStatsJob.addArgument(FastxQualityStatsCLI.INFILE, fastqFile.getAbsolutePath()); CondorJob perBaseStatJob = PipelineJobFactory.createJob(++count, PerBaseStatCLI.class, getWorkflowPlan(), htsfSample); perBaseStatJob.addArgument(PerBaseStatCLI.INFILE, fastxQualityStatsOutFile.getAbsolutePath()); CondorJob sequenceReadQualityFilter = PipelineJobFactory.createJob(++count, SequenceReadQualityFilterCLI.class, getWorkflowPlan(), htsfSample); sequenceReadQualityFilter.addArgument(SequenceReadQualityFilterCLI.INFILE, CondorJob bcTrendJob = PipelineJobFactory.createJob(++count, BCTrendCLI.class, getWorkflowPlan(), htsfSample); bcTrendJob.addArgument(BCTrendCLI.INFILE, fastxQualityStatsOutFile.getAbsolutePath()); CondorJob trimCountAdapterR1Job = PipelineJobFactory.createJob(++count, TrimCountAdapterCLI.class, getWorkflowPlan(), htsfSample); trimCountAdapterR1Job.addArgument(TrimCountAdapterCLI.INFASTQ, r1FastqFile.getAbsolutePath()); CondorJob bwaAlignR1Job = PipelineJobFactory.createJob(++count, BWAAlignCLI.class, getWorkflowPlan(), htsfSample); bwaAlignR1Job.addArgument(BWAAlignCLI.THREADS, "4"); CondorJob trimCountAdapterR2Job = PipelineJobFactory.createJob(++count, TrimCountAdapterCLI.class, getWorkflowPlan(), htsfSample); trimCountAdapterR2Job.addArgument(TrimCountAdapterCLI.INFASTQ, r2FastqFile.getAbsolutePath()); CondorJob bwaAlignR2Job = PipelineJobFactory.createJob(++count, BWAAlignCLI.class,
CondorJob helloJob = PipelineJobFactory.createJob(++count, EchoCLI.class, getWorkflowPlan(), null, false); CondorJob worldJob = PipelineJobFactory.createJob(++count, EchoCLI.class, getWorkflowPlan(), null, false); CondorJob catJob = PipelineJobFactory.createJob(++count, CatCLI.class, getWorkflowPlan(), null, false);