Merge pull request #334 from LabKey/fb_merge_24.11_to_develop

Merge discvr-24.11 to develop

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/SVTyperStep.java

@@ -113,6 +113,8 @@ else if (!svVcf.exists())
                 jsonArgs.add("-l");
                 jsonArgs.add(coverageJson.getPath());
 
+                jsonArgs.add("--verbose");
+
                 File doneFile = new File(ctx.getWorkingDirectory(), "json.done");
                 ctx.getFileManager().addIntermediateFile(doneFile);
                 if (doneFile.exists())
@@ -151,6 +153,8 @@ else if (!svVcf.exists())
                 svtyperArgs.add("-l");
                 svtyperArgs.add(coverageJson.getPath());
 
+                svtyperArgs.add("--verbose");
+
                 if (threads != null)
                 {
                     svtyperArgs.add("--core");

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -228,8 +228,17 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
             throw new PipelineJobException("Unable to find expected file: " + outputFile);
         }
 
+        String description = null;
+        if (kingCutoff != null)
+        {
+            long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id"));
+            long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id"));
+
+            description = String.format("KING cutoff: %f, included IDs: %d, excluded IDs: %d", kingCutoff, includedIds, excludedIds);
+        }
+
         output.addOutput(outputFile, "PLink PCA");
-        output.addSequenceOutput(outputFile, "PLink PCA for: " + inputVCF.getName() + (setName == null ? "" : ", for: " + setName), "PLink PCA", null, null, genome.getGenomeId(), null);
+        output.addSequenceOutput(outputFile, "PLink PCA for: " + inputVCF.getName() + (setName == null ? "" : ", for: " + setName), "PLink PCA", null, null, genome.getGenomeId(), description);
     }
 
     @Override

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java

@@ -8,6 +8,7 @@
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenomeManager;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 import org.labkey.api.util.FileUtil;
@@ -159,6 +160,8 @@ else if ("gbk".equalsIgnoreCase(ext))
         //params.add(basename);
 
         execute(params);
+
+        ReferenceGenomeManager.get().markGenomeModified(genome, getLogger());
     }
 
 

singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java

@@ -132,7 +132,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu
             ret.callerDisagreementThreshold = step.getProvider().getParameterByName("callerDisagreementThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             ret.doTSNE = step.getProvider().getParameterByName("doTSNE").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
             ret.doNotAllowResume = step.getProvider().getParameterByName("doNotAllowResume").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
-            ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true);
+            ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
             ret.failIfUnexpectedHtosFound = step.getProvider().getParameterByName("failIfUnexpectedHtosFound").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true);
             ret.htoReadset = htoReadset;
             ret.parentReadset = parentReadset;
@@ -177,7 +177,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse
             ret.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold");
             ret.doTSNE = params.optBoolean("doTSNE", false);
             ret.doNotAllowResume = params.optBoolean("doNotAllowResume", false);
-            ret.retainRawCountFile = params.optBoolean("retainRawCountFile", true);
+            ret.retainRawCountFile = params.optBoolean("retainRawCountFile", false);
             ret.failIfUnexpectedHtosFound = params.optBoolean("failIfUnexpectedHtosFound", true);
             ret.htoReadset = htoReadset;
             ret.parentReadset = parentReadset;