Program: 141123
Project: 141123
Buggy source:
@Override public StepResult execute(final StepContext context,final StepStatus status){
  final Data inData=context.getInputData(this.inputFormat);
  final Data outData=context.getOutputData(DataFormats.FASTQC_REPORT_HTML,inData);
  final DataFile inFile=inData.getDataFile(0);
  final DataFile reportFile=outData.getDataFile();
  SequenceFile seqFile=null;
  try {
    seqFile=SequenceFactory.getSequenceFile(inFile.toFile());
  }
 catch (  SequenceFormatException|IOException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
  final OverRepresentedSeqs os=new OverRepresentedSeqs();
  final List<AbstractQCModule> modules=Lists.newArrayList(new BasicStats(),new PerBaseQualityScores(),new PerTileQualityScores(),new PerSequenceQualityScores(),new PerBaseSequenceContent(),new PerSequenceGCContent(),new NContent(),new SequenceLengthDistribution(),os.duplicationLevelModule(),os,new AdapterContent(),new KmerContent());
  try {
    processSequences(modules,seqFile);
    createReport(modules,seqFile,reportFile.toFile());
    status.setDescription("String_Node_Str" + inData.getDataFile(0).toFile().getAbsolutePath() + "String_Node_Str"+ reportFile.getName()+ "String_Node_Str");
    modules.clear();
    return status.createStepResult();
  }
 catch (  final SequenceFormatException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
catch (  final IOException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
catch (  final XMLStreamException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
}

Fixed version (ground truth):
@Override public StepResult execute(final StepContext context,final StepStatus status){
  final Data inData=context.getInputData(this.inputFormat);
  final Data outData=context.getOutputData(DataFormats.FASTQC_REPORT_HTML,inData);
  final DataFile inFile;
  if (inData.getFormat().getMaxFilesCount() > 1) {
    inFile=inData.getDataFile(0);
  }
 else {
    inFile=inData.getDataFile();
  }
  final DataFile reportFile=outData.getDataFile();
  SequenceFile seqFile=null;
  try {
    seqFile=SequenceFactory.getSequenceFile(inFile.toFile());
  }
 catch (  SequenceFormatException|IOException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
  final OverRepresentedSeqs os=new OverRepresentedSeqs();
  final List<AbstractQCModule> modules=Lists.newArrayList(new BasicStats(),new PerBaseQualityScores(),new PerTileQualityScores(),new PerSequenceQualityScores(),new PerBaseSequenceContent(),new PerSequenceGCContent(),new NContent(),new SequenceLengthDistribution(),os.duplicationLevelModule(),os,new AdapterContent(),new KmerContent());
  try {
    processSequences(modules,seqFile);
    createReport(modules,seqFile,reportFile.toFile());
    status.setDescription("String_Node_Str" + inData.getDataFile(0).toFile().getAbsolutePath() + "String_Node_Str"+ reportFile.getName()+ "String_Node_Str");
    modules.clear();
    return status.createStepResult();
  }
 catch (  final SequenceFormatException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
catch (  final IOException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
catch (  final XMLStreamException e) {
    return status.createStepResult(e,"String_Node_Str" + e.getMessage());
  }
}