Examples with SomaticRunMetadata com.hartwig.pipeline.metadata.SomaticRunMetadata used on opensource projects

Example 6 with SomaticRunMetadata

use of com.hartwig.pipeline.metadata.SomaticRunMetadata in project pipeline5 by hartwigmedical.

the class FullPipelineTest method supportsSingleSampleIni.

@Ignore("May not support single sample")
@Test
public void supportsSingleSampleIni() throws Exception {
    SomaticRunMetadata metadata = TestInputs.defaultSingleSampleRunMetadata();
    when(api.get()).thenReturn(metadata);
    victim = new FullPipeline(reference, tumor, somatic, Executors.newCachedThreadPool(), referenceListener, tumorListener, api, cleanup);
    when(reference.run(metadata.reference())).then(callHandlers(referenceListener, TestInputs.referenceAlignmentOutput(), succeeded()));
    when(somatic.run(TestInputs.defaultPair())).thenReturn(succeeded());
    assertThat(victim.run().status()).isEqualTo(PipelineStatus.SUCCESS);
}