Examples with Lane com.hartwig.patient.Lane used on opensource projects

Example 1 with Lane

use of com.hartwig.patient.Lane in project pipeline5 by hartwigmedical.

the class BwaAligner method run.

public AlignmentOutput run(final SingleSampleRunMetadata metadata) throws Exception {
    StageTrace trace = new StageTrace(NAMESPACE, metadata.sampleName(), StageTrace.ExecutorType.COMPUTE_ENGINE).start();
    RuntimeBucket rootBucket = RuntimeBucket.from(storage, NAMESPACE, metadata, arguments, labels);
    Sample sample = sampleSource.sample(metadata);
    if (sample.bam().isPresent()) {
        String noPrefix = sample.bam().orElseThrow().replace("gs://", "");
        int firstSlash = noPrefix.indexOf("/");
        String bucket = noPrefix.substring(0, firstSlash);
        String path = noPrefix.substring(firstSlash + 1);
        return AlignmentOutput.builder().sample(metadata.sampleName()).status(PipelineStatus.PROVIDED).maybeAlignments(GoogleStorageLocation.of(bucket, path)).build();
    }
    final ResourceFiles resourceFiles = buildResourceFiles(arguments);
    sampleUpload.run(sample, rootBucket);
    List<Future<PipelineStatus>> futures = new ArrayList<>();
    List<GoogleStorageLocation> perLaneBams = new ArrayList<>();
    List<ReportComponent> laneLogComponents = new ArrayList<>();
    List<GoogleStorageLocation> laneFailedLogs = new ArrayList<>();
    for (Lane lane : sample.lanes()) {
        RuntimeBucket laneBucket = RuntimeBucket.from(storage, laneNamespace(lane), metadata, arguments, labels);
        BashStartupScript bash = BashStartupScript.of(laneBucket.name());
        InputDownload first = new InputDownload(GoogleStorageLocation.of(rootBucket.name(), fastQFileName(sample.name(), lane.firstOfPairPath())));
        InputDownload second = new InputDownload(GoogleStorageLocation.of(rootBucket.name(), fastQFileName(sample.name(), lane.secondOfPairPath())));
        bash.addCommand(first).addCommand(second);
        bash.addCommands(OverrideReferenceGenomeCommand.overrides(arguments));
        SubStageInputOutput alignment = new LaneAlignment(arguments.sbpApiRunId().isPresent(), resourceFiles.refGenomeFile(), first.getLocalTargetPath(), second.getLocalTargetPath(), metadata.sampleName(), lane).apply(SubStageInputOutput.empty(metadata.sampleName()));
        perLaneBams.add(GoogleStorageLocation.of(laneBucket.name(), resultsDirectory.path(alignment.outputFile().fileName())));
        bash.addCommands(alignment.bash()).addCommand(new OutputUpload(GoogleStorageLocation.of(laneBucket.name(), resultsDirectory.path()), RuntimeFiles.typical()));
        futures.add(executorService.submit(() -> runWithRetries(metadata, laneBucket, VirtualMachineJobDefinition.alignment(laneId(lane).toLowerCase(), bash, resultsDirectory))));
        laneLogComponents.add(new RunLogComponent(laneBucket, laneNamespace(lane), Folder.from(metadata), resultsDirectory));
        laneFailedLogs.add(GoogleStorageLocation.of(laneBucket.name(), RunLogComponent.LOG_FILE));
    }
    AlignmentOutput output;
    if (lanesSuccessfullyComplete(futures)) {
        List<InputDownload> laneBams = perLaneBams.stream().map(InputDownload::new).collect(Collectors.toList());
        BashStartupScript mergeMarkdupsBash = BashStartupScript.of(rootBucket.name());
        laneBams.forEach(mergeMarkdupsBash::addCommand);
        SubStageInputOutput merged = new MergeMarkDups(laneBams.stream().map(InputDownload::getLocalTargetPath).filter(path -> path.endsWith("bam")).collect(Collectors.toList())).apply(SubStageInputOutput.empty(metadata.sampleName()));
        mergeMarkdupsBash.addCommands(merged.bash());
        mergeMarkdupsBash.addCommand(new OutputUpload(GoogleStorageLocation.of(rootBucket.name(), resultsDirectory.path()), RuntimeFiles.typical()));
        PipelineStatus status = runWithRetries(metadata, rootBucket, VirtualMachineJobDefinition.mergeMarkdups(mergeMarkdupsBash, resultsDirectory));
        ImmutableAlignmentOutput.Builder outputBuilder = AlignmentOutput.builder().sample(metadata.sampleName()).status(status).maybeAlignments(GoogleStorageLocation.of(rootBucket.name(), resultsDirectory.path(merged.outputFile().fileName()))).addAllReportComponents(laneLogComponents).addAllFailedLogLocations(laneFailedLogs).addFailedLogLocations(GoogleStorageLocation.of(rootBucket.name(), RunLogComponent.LOG_FILE)).addReportComponents(new RunLogComponent(rootBucket, Aligner.NAMESPACE, Folder.from(metadata), resultsDirectory));
        if (!arguments.outputCram()) {
            outputBuilder.addReportComponents(new SingleFileComponent(rootBucket, Aligner.NAMESPACE, Folder.from(metadata), bam(metadata.sampleName()), bam(metadata.sampleName()), resultsDirectory), new SingleFileComponent(rootBucket, Aligner.NAMESPACE, Folder.from(metadata), bai(bam(metadata.sampleName())), bai(bam(metadata.sampleName())), resultsDirectory)).addDatatypes(new AddDatatype(DataType.ALIGNED_READS, metadata.barcode(), new ArchivePath(Folder.from(metadata), BwaAligner.NAMESPACE, bam(metadata.sampleName()))), new AddDatatype(DataType.ALIGNED_READS_INDEX, metadata.barcode(), new ArchivePath(Folder.from(metadata), BwaAligner.NAMESPACE, bai(metadata.sampleName()))));
        }
        output = outputBuilder.build();
    } else {
        output = AlignmentOutput.builder().sample(metadata.sampleName()).status(PipelineStatus.FAILED).build();
    }
    trace.stop();
    executorService.shutdown();
    return output;
}

Example 2 with Lane

use of com.hartwig.patient.Lane in project pipeline5 by hartwigmedical.

the class GoogleStorageSampleSource method sample.

@Override
public Sample sample(final SingleSampleRunMetadata metadata) {
    RuntimeBucket runtimeBucket = RuntimeBucket.from(storage, Aligner.NAMESPACE, metadata, arguments, labels);
    Iterable<Blob> blobs = runtimeBucket.list("samples/");
    if (Iterables.isEmpty(blobs)) {
        throw new IllegalArgumentException(String.format("No sample data found in bucket [%s] so there is no input to process. " + "You cannot use the upload=false flag if no sample has already been uploaded", runtimeBucket.name()));
    }
    String sampleDirectory = "/samples/" + metadata.barcode();
    String sampleNameWithPostfix = metadata.barcode();
    List<Lane> lanes = FastqFiles.toLanes(StreamSupport.stream(blobs.spliterator(), false).map(Blob::getName).map(File::new).map(File::getName).collect(Collectors.toList()), sampleDirectory, sampleNameWithPostfix);
    return Sample.builder(sampleNameWithPostfix).addAllLanes(lanes).build();
}

Example 3 with Lane

use of com.hartwig.patient.Lane in project pipeline5 by hartwigmedical.

the class JsonSampleSourceTest method simplePairParsedAndTumorReturned.

@Test
public void simplePairParsedAndTumorReturned() {
    JsonSampleSource victim = new JsonSampleSource(Resources.testResource("json_sample_source/single_lane.json"));
    Sample sample = victim.sample(TestInputs.tumorRunMetadata());
    assertThat(sample.name()).isEqualTo("CPCT12345678T");
    assertThat(sample.lanes()).hasSize(1);
    Lane lane = sample.lanes().get(0);
    assertThat(lane.firstOfPairPath()).isEqualTo("CPCT12345678T_R1.fastq");
    assertThat(lane.secondOfPairPath()).isEqualTo("CPCT12345678T_R2.fastq");
    assertThat(lane.laneNumber()).isEqualTo("1");
}

Example 4 with Lane

use of com.hartwig.patient.Lane in project pipeline5 by hartwigmedical.

the class JsonSampleSourceTest method simplePairParsedAndReferenceReturned.

@Test
public void simplePairParsedAndReferenceReturned() {
    JsonSampleSource victim = new JsonSampleSource(Resources.testResource("json_sample_source/single_lane.json"));
    Sample sample = victim.sample(TestInputs.referenceRunMetadata());
    assertThat(sample.name()).isEqualTo("CPCT12345678R");
    assertThat(sample.lanes()).hasSize(1);
    Lane lane = sample.lanes().get(0);
    assertThat(lane.firstOfPairPath()).isEqualTo("CPCT12345678R_R1.fastq");
    assertThat(lane.secondOfPairPath()).isEqualTo("CPCT12345678R_R2.fastq");
    assertThat(lane.laneNumber()).isEqualTo("1");
}

Example 5 with Lane

use of com.hartwig.patient.Lane in project pipeline5 by hartwigmedical.

the class GoogleStorageSampleSourceTest method verifyFastq.

private void verifyFastq(final String firstOfPair, final String secondOfPair) {
    Bucket bucket = mock(Bucket.class);
    Blob firstBlob = TestBlobs.blob(firstOfPair);
    Blob secondBlob = TestBlobs.blob(secondOfPair);
    Page<Blob> page = TestBlobs.pageOf(firstBlob, secondBlob);
    when(bucket.list(Storage.BlobListOption.prefix("aligner/samples/"))).thenReturn(page);
    when(storage.get(Mockito.anyString())).thenReturn(bucket);
    Sample sample = victim.sample(referenceRunMetadata());
    assertThat(sample.name()).isEqualTo(TestInputs.referenceSample());
    assertThat(sample.lanes()).hasSize(1);
    Lane lane = sample.lanes().get(0);
    assertThat(lane.firstOfPairPath()).isEqualTo(firstBlob.getName());
    assertThat(lane.secondOfPairPath()).isEqualTo(secondBlob.getName());
}