Update nimble arguments

Author: bbimber

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

@@ -57,9 +57,6 @@ public static List<ToolParameterDescriptor> getToolParameters()
                     put("initialValues", "unstranded");
                     put("delimiter", ";");
                 }}, null),
-                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),
                 ToolParameterDescriptor.create(MAX_HITS_TO_REPORT, "Max Hits To Report", "If a given hit has more than this number of references, it is discarded", "ldk-integerfield", new JSONObject(){{
                     put("minValue", 0);
                 }}, 4)

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

@@ -43,7 +43,6 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import static org.labkey.singlecell.run.NimbleAlignmentStep.ALIGN_OUTPUT;
 import static org.labkey.singlecell.run.NimbleAlignmentStep.MAX_HITS_TO_REPORT;
 import static org.labkey.singlecell.run.NimbleAlignmentStep.REF_GENOMES;
 import static org.labkey.singlecell.run.NimbleAlignmentStep.STRANDEDNESS;
@@ -425,14 +424,6 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
             alignArgs.add(String.valueOf(maxThreads));
         }
 
-        boolean alignOutput = getProvider().getParameterByName(ALIGN_OUTPUT).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
-        File alignmentOutputFile = new File(getPipelineCtx().getWorkingDirectory(), "nimbleAlignment." + (genomes.size() == 1 ? genomes.get(0).genomeId + "." : "") + "bam");
-        if (alignOutput)
-        {
-            alignArgs.add("--alignment_path");
-            alignArgs.add("/work/" + alignmentOutputFile.getName());
-        }
-
         String strandedness = getProvider().getParameterByName(STRANDEDNESS).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null);
         if (strandedness != null)
         {
@@ -451,13 +442,6 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         alignArgs.add("--input");
         alignArgs.add("/work/" + localBam.getName());
 
-        Integer maxRam = SequencePipelineService.get().getMaxRam();
-        if (maxRam != null)
-        {
-            alignArgs.add("-m");
-            alignArgs.add(maxRam + "000"); // in MB
-        }
-
         boolean dockerRan = runUsingDocker(alignArgs, output, "align.all");
         for (NimbleGenome genome : genomes)
         {