Add param to force re-processing of cell hashing

Author: bbimber

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

@@ -112,6 +112,7 @@ public static class CellHashingParameters
         public boolean keepMarkdown = false;
         public File h5File = null;
         public boolean doTSNE = false;
+        public boolean doNotAllowResume = false;
 
         private CellHashingParameters()
         {
@@ -128,6 +129,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu
             ret.minAllowableDoubletRateFilter = step.getProvider().getParameterByName("minAllowableDoubletRateFilter").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             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.failIfUnexpectedHtosFound = step.getProvider().getParameterByName("failIfUnexpectedHtosFound").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true);
             ret.htoReadset = htoReadset;
@@ -171,6 +173,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse
             ret.minAllowableDoubletRateFilter = params.get("minAllowableDoubletRateFilter") == null ? null : params.getDouble("minAllowableDoubletRateFilter");
             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.failIfUnexpectedHtosFound = params.optBoolean("failIfUnexpectedHtosFound", true);
             ret.htoReadset = htoReadset;

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -627,6 +627,12 @@ public File generateHashingCallsForRawMatrix(Readset parentReadset, PipelineOutp
         String outputBasename = parameters.getBasename() + "." + parameters.type.name();
         File callsFile = getExpectedCallsFile(ctx.getOutputDir(), outputBasename);
         File doneFile = new File(callsFile.getPath() + ".done");
+        if (doneFile.exists() & parameters.doNotAllowResume)
+        {
+            ctx.getLogger().debug("doneFile exists, but doNotAllowResume was selected");
+            doneFile.delete();
+        }
+
         if (!doneFile.exists())
         {
             callsFile = generateCellHashingCalls(rawCountMatrixDir, ctx.getOutputDir(), outputBasename, ctx.getLogger(), ctx.getSourceDirectory(), parameters);