Add support for nimble alignment output

Author: bbimber

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

@@ -51,6 +51,7 @@ public class NimbleAlignmentStep extends AbstractParameterizedOutputHandler<Sequ
     public static final String REF_GENOMES = "refGenomes";
     public static final String ALIGN_TEMPLATE = "alignTemplate";
     public static final String GROUP_BY_LINEAGE = "groupByLineage";
+    public static final String ALIGN_OUTPUT = "alignmentOutput";
 
     public NimbleAlignmentStep()
     {
@@ -66,6 +67,9 @@ public NimbleAlignmentStep()
                 }}, null),
                 ToolParameterDescriptor.create(GROUP_BY_LINEAGE, "Group By Lineage", "If checked, results will be aggregated by lineage", "checkbox", new JSONObject(){{
                     put("checked", true);
+                }}, true),
+                ToolParameterDescriptor.create(ALIGN_OUTPUT, "Create Alignment/Debug Output", "If checked, an alignment-level summary TSV will be created", "checkbox", new JSONObject(){{
+                    put("checked", true);
                 }}, true)
         ));
     }
@@ -304,6 +308,13 @@ private File doAlignment(JobContext ctx, int genomeId, File refJson, SequenceOut
             alignArgs.add("-l");
             alignArgs.add("/work/nimbleDebug.txt");
 
+            boolean debugOutput = ctx.getParams().optBoolean(ALIGN_OUTPUT, false);
+            if (debugOutput)
+            {
+                alignArgs.add("-a");
+                alignArgs.add("/work/nimbleAlignment.txt.gz");
+            }
+
             alignArgs.add("/work/" + localRefJson.getName());
             alignArgs.add("/work/" + resultsTsv.getName());
             alignArgs.add("/work/" + localBam.getName());