Refactor nimble to use DockerWrapper

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java

@@ -130,7 +130,7 @@ else if (!svVcf.exists())
                     SelectVariantsWrapper svw = new SelectVariantsWrapper(ctx.getLogger());
                     List<String> selectArgs = new ArrayList<>();
                     selectArgs.add("-select");
-                    selectArgs.add("SVTYPE != 'BND' && POS > 150 && !(vc.hasAttribute('SVTYPE') && vc.getAttribute('SVTYPE') == 'INS' && vc.hasSymbolicAlleles() && !vc.hasAttribute('SEQ'))");
+                    selectArgs.add("SVTYPE != 'BND' && SVTYPE != 'DUP' && POS > 150 && !(vc.hasAttribute('SVTYPE') && vc.getAttribute('SVTYPE') == 'INS' && vc.hasSymbolicAlleles() && !vc.hasAttribute('SEQ'))");
                     selectArgs.add("--exclude-filtered");
                     selectArgs.add("--exclude-filtered");
                     selectArgs.add("--sites-only-vcf-output");

singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java

@@ -115,8 +115,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 }
 
                 // This will update these files in-place:
-                File alignmentFileLocal = NimbleHelper.ensureLocalCopy(alignmentFile, output, ctx);
-                File reportFile = NimbleHelper.runNimbleReport(alignmentFileLocal, so.getLibrary_id(), output, ctx);
+                File reportFile = NimbleHelper.runNimbleReport(alignmentFile, so.getLibrary_id(), output, ctx);
                 if (!reportFile.exists())
                 {
                     throw new PipelineJobException("Unable to find file: " + reportFile.getPath());