Bugfix SRA download

Author: bbimber

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

@@ -1894,10 +1894,10 @@ private void restoreArchivedReadDataIfNeeded(Readset rs) throws PipelineJobExcep
                 RestoreSraDataHandler.FastqDumpWrapper sra = new RestoreSraDataHandler.FastqDumpWrapper(getJob().getLogger());
                 if (doneFile.exists())
                 {
-                    rdi.setFile(new File(outDir, rd.getSra_accession() + "_1.fastq"), 1);
+                    rdi.setFile(new File(outDir, rd.getSra_accession() + "_1.fastq.gz"), 1);
                     if (rd.getFileId2() != null)
                     {
-                        rdi.setFile(new File(outDir, rd.getSra_accession() + "_2.fastq"), 2);
+                        rdi.setFile(new File(outDir, rd.getSra_accession() + "_2.fastq.gz"), 2);
                     }
                 }
                 else

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

@@ -512,8 +512,11 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
             {
                 getLogger().info("Deleting extra files: ");
                 files.forEach(f -> {
-                    getLogger().info(f.getName());
-                    f.delete();
+                    if (f.exists())
+                    {
+                        getLogger().info(f.getName());
+                        f.delete();
+                    }
                 });
             }