diff --git a/cluster/src/main/java/com/hartwig/pipeline/tertiary/orange/Orange.java b/cluster/src/main/java/com/hartwig/pipeline/tertiary/orange/Orange.java
index bbda2cbbb..087b9d708 100644
--- a/cluster/src/main/java/com/hartwig/pipeline/tertiary/orange/Orange.java
+++ b/cluster/src/main/java/com/hartwig/pipeline/tertiary/orange/Orange.java
@@ -1,11 +1,5 @@
 package com.hartwig.pipeline.tertiary.orange;
 
-import static com.hartwig.pipeline.execution.vm.InputDownload.initialiseOptionalLocation;
-import static com.hartwig.pipeline.tools.HmfTool.ORANGE;
-
-import java.time.format.DateTimeFormatter;
-import java.util.List;
-
 import com.google.common.collect.ImmutableList;
 import com.hartwig.events.pipeline.Pipeline;
 import com.hartwig.pipeline.Arguments;
@@ -13,23 +7,13 @@
 import com.hartwig.pipeline.calling.sage.SageOutput;
 import com.hartwig.pipeline.datatypes.DataType;
 import com.hartwig.pipeline.execution.PipelineStatus;
-import com.hartwig.pipeline.execution.vm.BashCommand;
-import com.hartwig.pipeline.execution.vm.BashStartupScript;
-import com.hartwig.pipeline.execution.vm.InputDownload;
-import com.hartwig.pipeline.execution.vm.InputDownloadIfBlobExists;
-import com.hartwig.pipeline.execution.vm.VirtualMachineJobDefinition;
-import com.hartwig.pipeline.execution.vm.VirtualMachinePerformanceProfile;
-import com.hartwig.pipeline.execution.vm.VmDirectories;
+import com.hartwig.pipeline.execution.vm.*;
 import com.hartwig.pipeline.execution.vm.java.JavaJarCommand;
 import com.hartwig.pipeline.execution.vm.unix.MkDirCommand;
 import com.hartwig.pipeline.flagstat.FlagstatOutput;
 import com.hartwig.pipeline.input.SomaticRunMetadata;
 import com.hartwig.pipeline.metrics.BamMetricsOutput;
-import com.hartwig.pipeline.output.AddDatatype;
-import com.hartwig.pipeline.output.ArchivePath;
-import com.hartwig.pipeline.output.EntireOutputComponent;
-import com.hartwig.pipeline.output.Folder;
-import com.hartwig.pipeline.output.RunLogComponent;
+import com.hartwig.pipeline.output.*;
 import com.hartwig.pipeline.resource.ResourceFiles;
 import com.hartwig.pipeline.stages.Namespace;
 import com.hartwig.pipeline.stages.Stage;
@@ -39,11 +23,7 @@
 import com.hartwig.pipeline.tertiary.cuppa.CuppaOutput;
 import com.hartwig.pipeline.tertiary.cuppa.CuppaOutputLocations;
 import com.hartwig.pipeline.tertiary.lilac.LilacOutput;
-import com.hartwig.pipeline.tertiary.linx.LinxGermline;
-import com.hartwig.pipeline.tertiary.linx.LinxGermlineOutput;
-import com.hartwig.pipeline.tertiary.linx.LinxSomatic;
-import com.hartwig.pipeline.tertiary.linx.LinxSomaticOutput;
-import com.hartwig.pipeline.tertiary.linx.LinxSomaticOutputLocations;
+import com.hartwig.pipeline.tertiary.linx.*;
 import com.hartwig.pipeline.tertiary.peach.PeachOutput;
 import com.hartwig.pipeline.tertiary.purple.Purple;
 import com.hartwig.pipeline.tertiary.purple.PurpleOutput;
@@ -52,6 +32,12 @@
 import com.hartwig.pipeline.tertiary.virus.VirusInterpreterOutput;
 import com.hartwig.pipeline.tools.VersionUtils;
 
+import java.time.format.DateTimeFormatter;
+import java.util.List;
+
+import static com.hartwig.pipeline.execution.vm.InputDownload.initialiseOptionalLocation;
+import static com.hartwig.pipeline.tools.HmfTool.ORANGE;
+
 @Namespace(Orange.NAMESPACE)
 public class Orange implements Stage<OrangeOutput, SomaticRunMetadata> {
     public static final String NAMESPACE = "orange";
@@ -270,11 +256,15 @@ public OrangeOutput persistedOutput(final SomaticRunMetadata metadata) {
 
     @Override
     public List<AddDatatype> addDatatypes(final SomaticRunMetadata metadata) {
-        final String orangePdf = metadata.tumor().sampleName() + ORANGE_OUTPUT_PDF;
-        final String orangeJson = metadata.tumor().sampleName() + ORANGE_OUTPUT_JSON;
-        return List.of(new AddDatatype(DataType.ORANGE_OUTPUT_JSON,
-                        metadata.barcode(),
-                        new ArchivePath(Folder.root(), namespace(), orangeJson)),
-                new AddDatatype(DataType.ORANGE_OUTPUT_PDF, metadata.barcode(), new ArchivePath(Folder.root(), namespace(), orangePdf)));
+        if (includeGermline) {
+            final String orangePdf = metadata.tumor().sampleName() + ORANGE_OUTPUT_PDF;
+            final String orangeJson = metadata.tumor().sampleName() + ORANGE_OUTPUT_JSON;
+            return List.of(new AddDatatype(DataType.ORANGE_OUTPUT_JSON,
+                            metadata.barcode(),
+                            new ArchivePath(Folder.root(), namespace(), orangeJson)),
+                    new AddDatatype(DataType.ORANGE_OUTPUT_PDF, metadata.barcode(), new ArchivePath(Folder.root(), namespace(), orangePdf)));
+        } else {
+            return List.of();
+        }
     }
 }
diff --git a/cluster/src/test/java/com/hartwig/pipeline/tertiary/orange/OrangeTest.java b/cluster/src/test/java/com/hartwig/pipeline/tertiary/orange/OrangeTest.java
index b3c479b3d..6556e151e 100644
--- a/cluster/src/test/java/com/hartwig/pipeline/tertiary/orange/OrangeTest.java
+++ b/cluster/src/test/java/com/hartwig/pipeline/tertiary/orange/OrangeTest.java
@@ -1,13 +1,5 @@
 package com.hartwig.pipeline.tertiary.orange;
 
-import static com.hartwig.pipeline.testsupport.TestInputs.toolCommand;
-import static com.hartwig.pipeline.tools.HmfTool.ORANGE;
-
-import static org.assertj.core.api.AssertionsForInterfaceTypes.assertThat;
-
-import java.util.Arrays;
-import java.util.List;
-
 import com.google.common.collect.ImmutableList;
 import com.hartwig.events.pipeline.Pipeline;
 import com.hartwig.pipeline.datatypes.DataType;
@@ -19,13 +11,29 @@
 import com.hartwig.pipeline.stages.Stage;
 import com.hartwig.pipeline.tertiary.TertiaryStageTest;
 import com.hartwig.pipeline.testsupport.TestInputs;
-
 import org.junit.Test;
 
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import static com.hartwig.pipeline.testsupport.TestInputs.defaultSomaticRunMetadata;
+import static com.hartwig.pipeline.testsupport.TestInputs.toolCommand;
+import static com.hartwig.pipeline.tools.HmfTool.ORANGE;
+import static org.assertj.core.api.AssertionsForInterfaceTypes.assertThat;
+
 public class OrangeTest extends TertiaryStageTest<OrangeOutput> {
 
+    private static BashCommand orangeCommand(Orange victim) {
+        return victim.tumorReferenceCommands(TestInputs.defaultSomaticRunMetadata()).get(2);
+    }
+
     @Override
     protected Stage<OrangeOutput, SomaticRunMetadata> createVictim() {
+        return constructOrange(Pipeline.Context.DIAGNOSTIC, true);
+    }
+
+    private Orange constructOrange(final Pipeline.Context context, final boolean includeGermline) {
         return new Orange(TestInputs.tumorMetricsOutput(),
                 TestInputs.referenceMetricsOutput(),
                 TestInputs.tumorFlagstatOutput(),
@@ -42,8 +50,8 @@ protected Stage<OrangeOutput, SomaticRunMetadata> createVictim() {
                 TestInputs.peachOutput(),
                 TestInputs.sigsOutput(),
                 TestInputs.REF_GENOME_37_RESOURCE_FILES,
-                Pipeline.Context.DIAGNOSTIC,
-                true);
+                context,
+                includeGermline);
     }
 
     @Override
@@ -109,55 +117,23 @@ protected List<String> expectedCommands() {
 
     @Test
     public void shouldAddResearchDisclaimerWhenResearchContext() {
-        Orange victim = new Orange(TestInputs.tumorMetricsOutput(),
-                TestInputs.referenceMetricsOutput(),
-                TestInputs.tumorFlagstatOutput(),
-                TestInputs.referenceFlagstatOutput(),
-                TestInputs.sageSomaticOutput(),
-                TestInputs.sageGermlineOutput(),
-                TestInputs.purpleOutput(),
-                TestInputs.chordOutput(),
-                TestInputs.lilacOutput(),
-                TestInputs.linxGermlineOutput(),
-                TestInputs.linxSomaticOutput(),
-                TestInputs.cuppaOutput(),
-                TestInputs.virusInterpreterOutput(),
-                TestInputs.peachOutput(),
-                TestInputs.sigsOutput(),
-                TestInputs.REF_GENOME_37_RESOURCE_FILES,
-                Pipeline.Context.RESEARCH,
-                true);
+        Orange victim = constructOrange(Pipeline.Context.RESEARCH, true);
         assertThat(orangeCommand(victim).asBash()).contains("-add_disclaimer");
     }
 
-    private static BashCommand orangeCommand(Orange victim) {
-        return victim.tumorReferenceCommands(TestInputs.defaultSomaticRunMetadata()).get(2);
-    }
-
     @Test
     public void shouldAddGermlineToSomaticConversionAndChangeNamespaceWhenNotIncludeGermline() {
-        Orange victim = new Orange(TestInputs.tumorMetricsOutput(),
-                TestInputs.referenceMetricsOutput(),
-                TestInputs.tumorFlagstatOutput(),
-                TestInputs.referenceFlagstatOutput(),
-                TestInputs.sageSomaticOutput(),
-                TestInputs.sageGermlineOutput(),
-                TestInputs.purpleOutput(),
-                TestInputs.chordOutput(),
-                TestInputs.lilacOutput(),
-                TestInputs.linxGermlineOutput(),
-                TestInputs.linxSomaticOutput(),
-                TestInputs.cuppaOutput(),
-                TestInputs.virusInterpreterOutput(),
-                TestInputs.peachOutput(),
-                TestInputs.sigsOutput(),
-                TestInputs.REF_GENOME_37_RESOURCE_FILES,
-                Pipeline.Context.RESEARCH,
-                false);
+        Orange victim = constructOrange(Pipeline.Context.RESEARCH, false);
         assertThat(victim.namespace()).isEqualTo(Orange.NAMESPACE_NO_GERMLINE);
         assertThat(orangeCommand(victim).asBash()).contains("-convert_germline_to_somatic");
     }
 
+    @Test
+    public void shouldReturnNoFurtherOperationsWhenGermlineNotIncluded() {
+        Orange victim = constructOrange(Pipeline.Context.RESEARCH, false);
+        assertThat(victim.addDatatypes(defaultSomaticRunMetadata())).isEqualTo(Collections.emptyList());
+    }
+
     @Override
     protected boolean isEnabledOnShallowSeq() {
         return false;