Specify threads for trimmomatic instead of letting it detect

Author: bbimber

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

@@ -154,7 +154,7 @@ private void execute(List<String> params, ProcessBuilder.Redirect redirect, @Nul
             try (BufferedReader procReader = new BufferedReader(new InputStreamReader(redirect == null ? p.getInputStream() : p.getErrorStream(), StringUtilsLabKey.DEFAULT_CHARSET)))
             {
                 String line;
-                while (p.isAlive() && (line = procReader.readLine()) != null)
+                while ((line = procReader.readLine()) != null)
                 {
                     if (output != null)
                     {

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TrimmomaticWrapper.java

@@ -564,13 +564,13 @@ public List<String> getTrimmomaticParams(File input, @Nullable File input2, Stri
             params.add("-phred" +  FastqUtils.getQualityOffset(encoding));
         }
 
-        //NOTE: the tool auto-detects
-        //Integer threads = SequenceTaskHelper.getMaxThreads(job);
-        //if (threads != null)
-        //{
-        //    params.add("-threads"); //multi-threaded
-        //    params.add(threads.toString());
-        //}
+        Integer threads = SequenceTaskHelper.getMaxThreads(getLogger());
+        if (threads != null)
+        {
+            threads = Math.min(1, threads - 1); //account for reading of log
+            params.add("-threads");
+            params.add(threads.toString());
+        }
 
         params.add(input.getPath());
         if (input2 != null)
@@ -673,7 +673,7 @@ public void run()
                     boolean haveReportedInvalidHeader = false;
 
                     String line;
-                    while (p.isAlive() && (line = reader.readLine()) != null)
+                    while ((line = reader.readLine()) != null)
                     {
                         String[] cells = line.split(" ");
                         if (cells.length < 4)