@Override public void postRun() throws WorkflowException { logger.info("ENTERING postRun()"); Set<HTSFSample> htsfSampleSet = getAggregateHTSFSampleSet(); logger.info("htsfSampleSet.size(): {}", htsfSampleSet.size()); for (HTSFSample htsfSample : htsfSampleSet) { SaveBestMatchAttributeRunnable runnable = new SaveBestMatchAttributeRunnable(); runnable.setMapseqDAOBean(getWorkflowBeanService().getMaPSeqDAOBean()); runnable.setHtsfSampleId(htsfSample.getId()); Executors.newSingleThreadExecutor().execute(runnable); } }
System.out.println(String.format("Successfully saved sample: %s", sample.getId())); logger.info(sample.toString());
PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample .getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName());
PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample .getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName());
PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample .getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName());
PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample .getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, htsfSample.getName());
PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample.getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName);
picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.SORTORDER, PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample.getId() .toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName);
picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.SORTORDER, PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample.getId() .toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName);
PicardSortOrderType.COORDINATE.toString().toLowerCase()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, htsfSample .getId().toString()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName);