Examples with NoopPersistedDataset com.hartwig.pipeline.reruns.NoopPersistedDataset used on opensource projects

Example 1 with NoopPersistedDataset

use of com.hartwig.pipeline.reruns.NoopPersistedDataset in project pipeline5 by hartwigmedical.

the class PersistedAlignmentTest method returnsCramsInConventionalLocationIfNoPersistedAndUseCrams.

@Test
public void returnsCramsInConventionalLocationIfNoPersistedAndUseCrams() {
    PersistedAlignment victim = new PersistedAlignment(new NoopPersistedDataset(), Arguments.testDefaultsBuilder().useCrams(true).build());
    AlignmentOutput output = victim.run(TestInputs.referenceRunMetadata());
    assertThat(output.sample()).isEqualTo("reference");
    assertThat(output.status()).isEqualTo(PipelineStatus.PERSISTED);
    assertThat(output.alignments()).isEqualTo(GoogleStorageLocation.of("bucket", "set/reference/cram/reference.cram"));
}

Example 2 with NoopPersistedDataset

use of com.hartwig.pipeline.reruns.NoopPersistedDataset in project pipeline5 by hartwigmedical.

the class PurpleTest method shallowModeUsesLowDepthSettings.

@Test
public void shallowModeUsesLowDepthSettings() {
    Purple victim = new Purple(new RefGenome37ResourceFiles(), TestInputs.paveSomaticOutput(), TestInputs.paveGermlineOutput(), TestInputs.gripssSomaticProcessOutput(), TestInputs.amberOutput(), TestInputs.cobaltOutput(), new NoopPersistedDataset(), Arguments.testDefaultsBuilder().shallow(true).build());
    assertThat(victim.tumorReferenceCommands(input()).get(0).asBash()).contains("-highly_diploid_percentage 0.88 -somatic_min_purity_spread 0.1");
}

Example 3 with NoopPersistedDataset

use of com.hartwig.pipeline.reruns.NoopPersistedDataset in project pipeline5 by hartwigmedical.

the class PipelineMain method start.

public PipelineState start(final Arguments arguments) {
    LOGGER.info("Arguments are [{}]", arguments);
    Versions.printAll();
    try {
        GoogleCredentials credentials = CredentialProvider.from(arguments).get();
        Storage storage = StorageProvider.from(arguments, credentials).get();
        Publisher turquoisePublisher = PublisherProvider.from(arguments, credentials).get("turquoise.events");
        Publisher pipelinePublisher = PublisherProvider.from(arguments, credentials).get(PipelineComplete.TOPIC);
        SomaticMetadataApi somaticMetadataApi = SomaticMetadataApiProvider.from(arguments, storage, pipelinePublisher).get();
        SingleSampleEventListener referenceEventListener = new SingleSampleEventListener();
        SingleSampleEventListener tumorEventListener = new SingleSampleEventListener();
        SomaticRunMetadata somaticRunMetadata = somaticMetadataApi.get();
        InputMode mode = new ModeResolver().apply(somaticRunMetadata);
        LOGGER.info("Starting pipeline in [{}] mode", mode);
        String ini = somaticRunMetadata.isSingleSample() ? "single_sample" : arguments.shallow() ? "shallow" : "somatic";
        PipelineProperties eventSubjects = PipelineProperties.builder().sample(somaticRunMetadata.maybeTumor().map(SingleSampleRunMetadata::sampleName).orElseGet(() -> somaticRunMetadata.reference().sampleName())).runId(arguments.sbpApiRunId()).set(somaticRunMetadata.set()).referenceBarcode(somaticRunMetadata.maybeReference().map(SingleSampleRunMetadata::barcode)).tumorBarcode(somaticRunMetadata.maybeTumor().map(SingleSampleRunMetadata::barcode)).type(ini).build();
        somaticMetadataApi.start();
        startedEvent(eventSubjects, turquoisePublisher, arguments.publishToTurquoise());
        BlockingQueue<BamMetricsOutput> referenceBamMetricsOutputQueue = new ArrayBlockingQueue<>(1);
        BlockingQueue<BamMetricsOutput> tumorBamMetricsOutputQueue = new ArrayBlockingQueue<>(1);
        BlockingQueue<FlagstatOutput> referenceFlagstatOutputQueue = new ArrayBlockingQueue<>(1);
        BlockingQueue<FlagstatOutput> tumorFlagstatOutputQueue = new ArrayBlockingQueue<>(1);
        BlockingQueue<GermlineCallerOutput> germlineCallerOutputQueue = new ArrayBlockingQueue<>(1);
        StartingPoint startingPoint = new StartingPoint(arguments);
        PersistedDataset persistedDataset = arguments.biopsy().<PersistedDataset>map(b -> new ApiPersistedDataset(SbpRestApi.newInstance(arguments.sbpApiUrl()), ObjectMappers.get(), b, arguments.project())).orElse(new NoopPersistedDataset());
        PipelineState state = new FullPipeline(singleSamplePipeline(arguments, credentials, storage, referenceEventListener, somaticRunMetadata, referenceBamMetricsOutputQueue, germlineCallerOutputQueue, referenceFlagstatOutputQueue, startingPoint, persistedDataset, mode), singleSamplePipeline(arguments, credentials, storage, tumorEventListener, somaticRunMetadata, tumorBamMetricsOutputQueue, germlineCallerOutputQueue, tumorFlagstatOutputQueue, startingPoint, persistedDataset, mode), somaticPipeline(arguments, credentials, storage, somaticRunMetadata, referenceBamMetricsOutputQueue, tumorBamMetricsOutputQueue, referenceFlagstatOutputQueue, tumorFlagstatOutputQueue, startingPoint, persistedDataset, mode), Executors.newCachedThreadPool(), referenceEventListener, tumorEventListener, somaticMetadataApi, CleanupProvider.from(arguments, storage).get()).run();
        completedEvent(eventSubjects, turquoisePublisher, state.status().toString(), arguments.publishToTurquoise());
        VmExecutionLogSummary.ofFailedStages(storage, state);
        return state;
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}

Example 4 with NoopPersistedDataset

use of com.hartwig.pipeline.reruns.NoopPersistedDataset in project pipeline5 by hartwigmedical.

the class PersistedAlignmentTest method returnsBamsInConventionalLocationIfNoPersisted.

@Test
public void returnsBamsInConventionalLocationIfNoPersisted() {
    PersistedAlignment victim = new PersistedAlignment(new NoopPersistedDataset(), Arguments.testDefaults());
    AlignmentOutput output = victim.run(TestInputs.referenceRunMetadata());
    assertThat(output.sample()).isEqualTo("reference");
    assertThat(output.status()).isEqualTo(PipelineStatus.PERSISTED);
    assertThat(output.alignments()).isEqualTo(GoogleStorageLocation.of("bucket", "set/reference/aligner/reference.bam"));
}

Example 5 with NoopPersistedDataset

use of com.hartwig.pipeline.reruns.NoopPersistedDataset in project pipeline5 by hartwigmedical.

the class SageSomaticCallerTest method shallowModeUsesHotspotQualOverride.

@Test
public void shallowModeUsesHotspotQualOverride() {
    SageSomaticCaller victim = new SageSomaticCaller(TestInputs.defaultPair(), new NoopPersistedDataset(), TestInputs.REF_GENOME_37_RESOURCE_FILES, Arguments.testDefaultsBuilder().shallow(true).build());
    assertThat(victim.tumorReferenceCommands(input()).get(0).asBash()).contains("-hotspot_min_tumor_qual 40");
}