Examples with Folder com.hartwig.pipeline.report.Folder used on opensource projects

Example 1 with Folder

use of com.hartwig.pipeline.report.Folder in project pipeline5 by hartwigmedical.

the class CramConversion method output.

@Override
public CramOutput output(final SingleSampleRunMetadata metadata, final PipelineStatus jobStatus, final RuntimeBucket bucket, final ResultsDirectory resultsDirectory) {
    String cram = new File(outputCram).getName();
    String crai = FileTypes.crai(cram);
    Folder folder = Folder.from(metadata);
    return CramOutput.builder().status(jobStatus).addFailedLogLocations(GoogleStorageLocation.of(bucket.name(), RunLogComponent.LOG_FILE)).addReportComponents(new RunLogComponent(bucket, NAMESPACE, folder, resultsDirectory), new StartupScriptComponent(bucket, NAMESPACE, folder), new SingleFileComponent(bucket, NAMESPACE, folder, cram, cram, resultsDirectory), new SingleFileComponent(bucket, NAMESPACE, folder, crai, crai, resultsDirectory)).addDatatypes(new AddDatatype(DataType.ALIGNED_READS, metadata.barcode(), new ArchivePath(Folder.from(metadata), namespace(), cram)), new AddDatatype(DataType.ALIGNED_READS_INDEX, metadata.barcode(), new ArchivePath(Folder.from(metadata), namespace(), crai))).build();
}