Fix inverted logic on whether we are running in single sample

hartwigmedical · Dec 5, 2019 · d7f5e93 · d7f5e93
1 parent 3b678d3
commit d7f5e93
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/cluster/src/main/java/com/hartwig/pipeline/PipelineMain.java b/cluster/src/main/java/com/hartwig/pipeline/PipelineMain.java
@@ -1,5 +1,7 @@
 package com.hartwig.pipeline;
 
+import java.util.concurrent.Executors;
+
 import com.google.auth.oauth2.GoogleCredentials;
 import com.google.cloud.storage.Storage;
 import com.hartwig.pipeline.alignment.AlignerProvider;
@@ -19,12 +21,11 @@
 import com.hartwig.pipeline.storage.RuntimeBucket;
 import com.hartwig.pipeline.storage.StorageProvider;
 import com.hartwig.pipeline.tools.Versions;
+
 import org.apache.commons.cli.ParseException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.concurrent.Executors;
-
 public class PipelineMain {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(PipelineMain.class);
@@ -38,9 +39,9 @@ public PipelineState start(Arguments arguments) {
             SomaticMetadataApi somaticMetadataApi = SomaticMetadataApiProvider.from(arguments, storage).get();
             SingleSampleEventListener referenceEventListener = new SingleSampleEventListener();
             SingleSampleEventListener tumorEventListener = new SingleSampleEventListener();
-            boolean isStandalone = !somaticMetadataApi.get().isSingleSample();
-            return new FullPipeline(singleSamplePipeline(arguments, credentials, storage, referenceEventListener, isStandalone),
-                    singleSamplePipeline(arguments, credentials, storage, tumorEventListener, isStandalone),
+            boolean isSingleSample = somaticMetadataApi.get().isSingleSample();
+            return new FullPipeline(singleSamplePipeline(arguments, credentials, storage, referenceEventListener, isSingleSample),
+                    singleSamplePipeline(arguments, credentials, storage, tumorEventListener, isSingleSample),
                     somaticPipeline(arguments, credentials, storage, somaticMetadataApi),
                     Executors.newCachedThreadPool(),
                     referenceEventListener,

diff --git a/cluster/src/main/java/com/hartwig/pipeline/metadata/SbpSomaticMetadataApi.java b/cluster/src/main/java/com/hartwig/pipeline/metadata/SbpSomaticMetadataApi.java
@@ -69,7 +69,7 @@ public SomaticRunMetadata get() {
                 SingleSampleRunMetadata tumor = find(TUMOR, samplesBySet).map(referenceSample -> toMetadata(referenceSample,
                         SingleSampleRunMetadata.SampleType.TUMOR))
                         .orElseThrow((() -> new IllegalStateException(String.format(
-                                "No tumor sample found in SBP for set [%s] and this run " + "was not marked as single sample",
+                                "No tumor sample found in SBP for set [%s] and this run was not marked as single sample",
                                 sbpSet.name()))));
                 return SomaticRunMetadata.builder().runName(sbpSet.name()).reference(reference).maybeTumor(tumor).build();
             }

diff --git a/cluster/src/main/java/com/hartwig/pipeline/report/PipelineResults.java b/cluster/src/main/java/com/hartwig/pipeline/report/PipelineResults.java
@@ -54,10 +54,10 @@ public void compose(SomaticRunMetadata metadata) {
         writeComplete(name);
     }
 
-    public void compose(SingleSampleRunMetadata metadata,  Boolean isStandalone, PipelineState state) {
+    public void compose(SingleSampleRunMetadata metadata,  Boolean isSingleSample, PipelineState state) {
         String name = RunTag.apply(arguments, metadata.sampleId());
         if (state.shouldProceed()) {
-            Folder folder = isStandalone ? Folder.from() : Folder.from(metadata);
+            Folder folder = isSingleSample ? Folder.from() : Folder.from(metadata);
             writeMetadata(metadata, name, folder);
             compose(name, folder);
         }