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

Example 1 with ZippedVcfAndIndexComponent

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

the class Gripss method output.

@Override
public GripssOutput output(final SomaticRunMetadata metadata, final PipelineStatus jobStatus, final RuntimeBucket bucket, final ResultsDirectory resultsDirectory) {
    String filteredVcfFile = filteredVcf(metadata);
    String unfilteredVcfFile = unfilteredVcf(metadata);
    return GripssOutput.builder(namespace()).status(jobStatus).maybeFilteredVariants(GoogleStorageLocation.of(bucket.name(), resultsDirectory.path(basename(filteredVcfFile)))).maybeUnfilteredVariants(GoogleStorageLocation.of(bucket.name(), resultsDirectory.path(basename(unfilteredVcfFile)))).addFailedLogLocations(GoogleStorageLocation.of(bucket.name(), RunLogComponent.LOG_FILE)).addReportComponents(new ZippedVcfAndIndexComponent(bucket, namespace(), Folder.root(), basename(unfilteredVcfFile), basename(unfilteredVcfFile), resultsDirectory)).addReportComponents(new ZippedVcfAndIndexComponent(bucket, namespace(), Folder.root(), basename(filteredVcfFile), basename(filteredVcfFile), resultsDirectory)).addReportComponents(new RunLogComponent(bucket, namespace(), Folder.root(), resultsDirectory)).addReportComponents(new StartupScriptComponent(bucket, namespace(), Folder.root())).addDatatypes(new AddDatatype(unfilteredDatatype(), metadata.barcode(), new ArchivePath(Folder.root(), namespace(), basename(unfilteredVcfFile))), new AddDatatype(filteredDatatype(), metadata.barcode(), new ArchivePath(Folder.root(), namespace(), basename(filteredVcfFile)))).build();
}