Add pangolin to COVID analysis

Author: bbimber

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

@@ -591,9 +591,25 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
 
         PindelAnalysis.runPindel(output, getPipelineCtx(), rs, outputDir, inputBam, referenceGenome.getWorkingFastaFile(), minFraction, minDepth, true, coverageOut, minInsertSize);
 
+        runPangolin(consensusFastaLoFreq);
+
         return output;
     }
 
+    private void runPangolin(File consensusFasta) throws PipelineJobException
+    {
+        SimpleScriptWrapper wrapper = new SimpleScriptWrapper(getPipelineCtx().getLogger());
+        wrapper.setWorkingDir(consensusFasta.getParentFile());
+
+        File pangolin = SequencePipelineService.get().getExeForPackage("PANGOLINPATH", "pangolin");
+
+        List<String> args = new ArrayList<>();
+        args.add(pangolin.getPath());
+        args.add(consensusFasta.getPath());
+
+        wrapper.execute(args);
+    }
+
     private File generateConsensus(File loFreqConsensusVcf, File fasta, File maskBed) throws PipelineJobException
     {
         File ret = new File(loFreqConsensusVcf.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(loFreqConsensusVcf.getName()) + ".fasta");