String r1FastqRootName = PipelineUtil.getRootFastqName(r1FastqFile.getName()); String r2FastqRootName = PipelineUtil.getRootFastqName(r2FastqFile.getName());
for (File fastqFile : readPairList) { String fastqRootName = PipelineUtil.getRootFastqName(fastqFile.getName()); String r1FastqRootName = PipelineUtil.getRootFastqName(r1FastqFile.getName()); String r2FastqRootName = PipelineUtil.getRootFastqName(r2FastqFile.getName());