Add option to keep VCF calls for DeepVariant

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/DeepVariantHandler.java

@@ -97,6 +97,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             action.addInput(so.getFile(), "Input BAM File");
 
             File outputFile = new File(ctx.getOutputDir(), FileUtil.getBaseName(so.getFile()) + ".g.vcf.gz");
+            File outputFileVcf = new File(ctx.getOutputDir(), FileUtil.getBaseName(so.getFile()) + ".vcf.gz");
 
             DeepVariantAnalysis.DeepVariantWrapper wrapper = new DeepVariantAnalysis.DeepVariantWrapper(job.getLogger());
             wrapper.setOutputDir(ctx.getOutputDir());
@@ -123,7 +124,8 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 throw new PipelineJobException("Missing binVersion");
             }
 
-            wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, ctx.getFileManager(), binVersion, args);
+            boolean retainVcf = ctx.getParams().optBoolean("retainVcf", false);
+            wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, retainVcf, ctx.getFileManager(), binVersion, args);
 
             action.addOutput(outputFile, "gVCF File", false);
 
@@ -137,6 +139,19 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             ctx.addSequenceOutput(o);
 
+            if (retainVcf)
+            {
+                SequenceOutputFile vcf = new SequenceOutputFile();
+                vcf.setName(outputFileVcf.getName());
+                vcf.setFile(outputFileVcf);
+                vcf.setLibrary_id(so.getLibrary_id());
+                vcf.setCategory("DeepVariant VCF File");
+                vcf.setReadset(so.getReadset());
+                vcf.setDescription("DeepVariant Version: " + binVersion);
+
+                ctx.addSequenceOutput(vcf);
+            }
+
             ctx.addActions(action);
         }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java

@@ -70,7 +70,8 @@ public static List<ToolParameterDescriptor> getToolDescriptors()
                 }}, "X,Y"),
                 ToolParameterDescriptor.create("binVersion", "DeepVariant Version", "The version of DeepVariant to run, which is passed to their docker container", "textfield", new JSONObject(){{
                     put("allowBlank", false);
-                }}, "1.6.0")
+                }}, "1.6.0"),
+                ToolParameterDescriptor.create("retainVcf", "Retain VCF", "If selected, the VCF with called genotypes will be retained", "checkbox", null, false)
         );
     }
 
@@ -153,9 +154,11 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
             throw new PipelineJobException("Missing binVersion");
         }
 
+        boolean retainVcf = getProvider().getParameterByName("retainVcf").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+
         getWrapper().setOutputDir(outputDir);
         getWrapper().setWorkingDir(outputDir);
-        getWrapper().execute(inputBam, referenceGenome.getWorkingFastaFile(), outputFile, output, binVersion, args);
+        getWrapper().execute(inputBam, referenceGenome.getWorkingFastaFile(), outputFile, retainVcf, output, binVersion, args);
 
         output.addOutput(outputFile, "gVCF File");
         output.addSequenceOutput(outputFile, outputFile.getName(), "DeepVariant gVCF File", rs.getReadsetId(), null, referenceGenome.getGenomeId(), "DeepVariant Version: " + binVersion);
@@ -164,6 +167,17 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
             output.addOutput(idxFile, "VCF Index");
         }
 
+        if (retainVcf)
+        {
+            File outputFileVcf = new File(outputDir, FileUtil.getBaseName(inputBam) + ".vcf.gz");
+            if (!outputFileVcf.exists())
+            {
+                throw new PipelineJobException("Missing expected file: " + outputFileVcf.getPath());
+            }
+
+            output.addSequenceOutput(outputFile, outputFileVcf.getName(), "DeepVariant VCF File", rs.getReadsetId(), null, referenceGenome.getGenomeId(), "DeepVariant Version: " + binVersion);
+        }
+
         return output;
     }
 
@@ -206,12 +220,15 @@ private File ensureLocalCopy(File input, File workingDirectory, PipelineOutputTr
             }
         }
 
-        public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutputTracker tracker, String binVersion, List<String> extraArgs) throws PipelineJobException
+        public void execute(File inputBam, File refFasta, File outputGvcf, boolean retainVcf, PipelineOutputTracker tracker, String binVersion, List<String> extraArgs) throws PipelineJobException
         {
             File workDir = outputGvcf.getParentFile();
             File outputVcf = new File(outputGvcf.getPath().replaceAll(".g.vcf", ".vcf"));
-            tracker.addIntermediateFile(outputVcf);
-            tracker.addIntermediateFile(new File(outputVcf.getPath() + ".tbi"));
+            if (!retainVcf)
+            {
+                tracker.addIntermediateFile(outputVcf);
+                tracker.addIntermediateFile(new File(outputVcf.getPath() + ".tbi"));
+            }
 
             File inputBamLocal = ensureLocalCopy(inputBam, workDir, tracker);
             ensureLocalCopy(SequenceUtil.getExpectedIndex(inputBam), workDir, tracker);