Delete downloaded SRA files once done

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java

@@ -110,11 +110,6 @@ public ProcessBuilder getProcessBuilder(List<String> params)
 
         if (!_environment.isEmpty())
         {
-            for (String var : _environment.keySet())
-            {
-                getLogger().debug("adding to env: " + var + " = " + _environment.get(var));
-            }
-
             pb.environment().putAll(_environment);
         }
 

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

@@ -203,6 +203,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                     {
                         ctx.getLogger().info("Copying file to: " + expectedFile1.getPath());
                         Files.copy(files.first.toPath(), expectedFile1.toPath());
+                        ctx.getFileManager().addIntermediateFile(files.first);
                         if (expectedFile2 != null)
                         {
                             if (files.second == null)
@@ -212,6 +213,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
 
                             ctx.getLogger().info("Copying file to: " + expectedFile2.getPath());
                             Files.copy(files.second.toPath(), expectedFile2.toPath());
+                            ctx.getFileManager().addIntermediateFile(files.second);
                         }
                     }
                     catch (IOException e)