File htsfSampleOutputDir = new File(workflowDir, htsfSample.getName()); File tmpDir = new File(htsfSampleOutputDir, "tmp"); tmpDir.mkdirs();
sb.append(String.format("HTSFSample Name: %s%n", sample.getName()));
Element meanQualityScorePassingFilteringElement = tdIter.next(); if (sample.getName().equals(sampleIdElement.text()) && sample.getLaneIndex().toString().equals(laneElement.text()) && sample.getBarcode().equals(indexElement.text())) {
File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes"); File outputDirectory = new File(workflowDir, htsfSample.getName());
File sequencerRunOutputDirectory = new File(baseDir, sequencerRun.getName()); File workflowDir = new File(sequencerRunOutputDirectory, "NCGenes"); File outputDirectory = new File(workflowDir, htsfSample.getName());
String oldSampleName = htsfSample.getName();
continue; htsfSampleNameSet.add(htsfSample.getName());
.getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName()); graph.addVertex(picardAddOrReplaceReadGroupsJob); graph.addEdge(samtoolsViewJob, picardAddOrReplaceReadGroupsJob);
.getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName()); graph.addVertex(picardAddOrReplaceReadGroupsJob); graph.addEdge(samtoolsViewJob, picardAddOrReplaceReadGroupsJob);
.getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName()); graph.addVertex(picardAddOrReplaceReadGroupsJob); graph.addEdge(samtoolsViewJob, picardAddOrReplaceReadGroupsJob);
.getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName()); graph.addVertex(picardAddOrReplaceReadGroupsJob); graph.addEdge(samtoolsViewJob, picardAddOrReplaceReadGroupsJob);