Drop --include-technical

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java

@@ -2022,7 +2022,7 @@ else if (sraIDs.contains(rd.getSra_accession()))
                             outDir.mkdirs();
                         }
 
-                        Pair<File, File> downloaded = sra.downloadSra(rd.getSra_accession(), unzippedOutDir, rd.isPairedEnd());
+                        Pair<File, File> downloaded = sra.downloadSra(rd.getSra_accession(), unzippedOutDir, rd.isPairedEnd(), false);
                         File moved1 = new File(outDir, downloaded.first.getName());
                         if (moved1.exists())
                         {

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java

@@ -384,7 +384,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                     File expectedFile2 = rd.getFileId2() == null ? null : ctx.getSequenceSupport().getCachedData(rd.getFileId2());
 
                     FastqDumpWrapper wrapper = new FastqDumpWrapper(ctx.getLogger());
-                    Pair<File, File> files = wrapper.downloadSra(accession, ctx.getOutputDir(), rd.isPairedEnd());
+                    Pair<File, File> files = wrapper.downloadSra(accession, ctx.getOutputDir(), rd.isPairedEnd(), false);
 
                     long lines1 = SequenceUtil.getLineCount(files.first) / 4;
                     ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1);
@@ -459,13 +459,16 @@ public FastqDumpWrapper(@Nullable Logger logger)
             super(logger);
         }
 
-        public Pair<File, File> downloadSra(String dataset, File outDir, boolean expectPaired) throws PipelineJobException
+        public Pair<File, File> downloadSra(String dataset, File outDir, boolean expectPaired, boolean includeTechnical) throws PipelineJobException
         {
             List<String> args = new ArrayList<>();
             args.add(getExe().getPath());
 
             // NOTE: we probably want the --split-3 behavior, which is the default for fasterq-dump
-            args.add("--include-technical");
+            if (includeTechnical)
+            {
+                args.add("--include-technical");
+            }
 
             Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());
             if (threads != null)