Merge pull request #179 from BimberLab/22.11_fb_merge

bbimber · web-flow · commit cd22e7af88ab · 2022-11-22T05:27:31.000-08:00
Merge discvr-22.7 to discvr-22.11
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
@@ -159,7 +159,7 @@ else if (_scatterGatherMethod == VariantProcessingStep.ScatterGatherMethod.fixed
 
     public boolean doAllowSplitContigs()
     {
-        return getParameterJson().optBoolean("scatterGather.allowSplitChromosomes", true);
+        return getParameterJson().optBoolean("scatterGather.allowSplitChromosomes", false);
     }
 
     public boolean isScatterJob()
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java
@@ -248,7 +248,7 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno
 
                 for (File s : inputs)
                 {
-                    String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' | awk ' { $1 == \"" + contig + "\" } ' | wc -l")));
+                    String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' | awk ' $1 == \"" + contig + "\" ' | wc -l")));
                     if ("0".equals(ret))
                     {
                         ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());
diff --git a/singlecell/resources/chunks/ClrNormalizeByGroup.R b/singlecell/resources/chunks/ClrNormalizeByGroup.R
@@ -1,7 +1,7 @@
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
-    seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureInclusionList = featureWhitelist, featureExclusionList = featureExclusionList)
+    seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureInclusionList = featureWhitelist, featureExclusionList = featureExclusionList, doAsinhTransform = doAsinhTransform)
 
     saveData(seuratObj, datasetId)
 
diff --git a/singlecell/resources/chunks/Functions.R b/singlecell/resources/chunks/Functions.R
@@ -64,6 +64,7 @@ savedFiles <- data.frame(datasetId = character(), datasetName = character(), fil
 if (file.exists('/work/savedSeuratObjects.txt')) {
     unlink('/work/savedSeuratObjects.txt')
 }
+file.create('/work/savedSeuratObjects.txt')
 
 saveData <- function(seuratObj, datasetId) {
     print(paste0('Saving dataset: ', datasetId))
diff --git a/singlecell/resources/chunks/RunScGate.R b/singlecell/resources/chunks/RunScGate.R
@@ -3,9 +3,9 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
     if (useRhesusDefaults) {
-        seuratObj <- RIRA::RunScGateWithRhesusModels(seuratObj, dropAmbiguousConsensusValues = dropAmbiguousConsensusValues)
+        seuratObj <- RIRA::RunScGateWithRhesusModels(seuratObj, dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, assay = assayName)
     } else {
-        seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels)
+        seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels, assay = assayName)
     }
 
     saveData(seuratObj, datasetId)
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateUCellScores.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateUCellScores.java
@@ -25,7 +25,7 @@ public Provider()
                     SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
 
                     }}, false),
-                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
 
                     }}, "RNA")
             ), null, null);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqDimReduxDist.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqDimReduxDist.java
@@ -23,7 +23,7 @@ public Provider()
                     SeuratToolParameter.create("performClrNormalization", "Perform CLR Normalization", "If true, Seurat CLR normalization will be performed. Otherwise any pre-existing normalization is used.", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true, "performClrNormalization", true),
-                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textfield", new JSONObject(){{
 
                     }}, "ADT")
             ), null, null);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqDimReduxPca.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqDimReduxPca.java
@@ -33,7 +33,7 @@ public Provider()
                         put("delimiter", ",");
                         put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
-                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textfield", new JSONObject(){{
 
                     }}, "ADT")
             ), null, null);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java
@@ -20,7 +20,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("CiteSeqPlots", "CiteSeq/ADT Plots", "CellMembrane/Seurat", "This will create FeaturePlots for all features in the ADT assay.", Arrays.asList(
-                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textfield", new JSONObject(){{
 
                     }}, "ADT")
             ), null, null);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ClrNormalizeByGroup.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ClrNormalizeByGroup.java
@@ -35,7 +35,10 @@ public Provider()
                     SeuratToolParameter.create("minCellsPerGroup", "Min Cells Per Group", "Any group with fewer than this many cells will be dropped.", "ldk-integerfield", new JSONObject(){{
 
                     }}, 20),
-                    SeuratToolParameter.create("calculatePerFeatureUCell", "Calculate Per Feature UCell ", "If checked, UCell will be run over each ", "checkbox", new JSONObject(){{
+                    SeuratToolParameter.create("calculatePerFeatureUCell", "Calculate Per Feature UCell ", "If checked, UCell will be run over each ADT", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("doAsinhTransform", "Do asinh Transform ", "If checked, count data will be transformed using asinh prior to CLR", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true),
                     SeuratToolParameter.create("featureWhitelist", "Genes to Add to VariableFeatures", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CustomUCell.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CustomUCell.java
@@ -34,7 +34,7 @@ public Provider()
                     SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
 
                     }}, false),
-                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
 
                     }}, "RNA")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PlotAverageCiteSeqCounts.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PlotAverageCiteSeqCounts.java
@@ -28,7 +28,7 @@ public Provider()
                         put("delimiter", ",");
                         put("stripCharsRe", "/(^['\"]+)|(['\"]+$)/g");
                     }}, "ClusterNames_0.2,ClusterNames_0.4,ClusterNames_0.6").delimiter(","),
-                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textfield", new JSONObject(){{
 
                     }}, "ADT")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunScGate.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunScGate.java
@@ -41,7 +41,10 @@ public Provider()
                     }}, null, null, true, true),
                     SeuratToolParameter.create("dropAmbiguousConsensusValues", "Drop Ambiguous Consensus Values", "If checked, any consensus calls that are ambiguous will be set to NA", "checkbox", new JSONObject(){{
                         put("checked", true);
-                    }}, true)
+                    }}, true),
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
+
+                    }}, "RNA")
                 ), null, null);
         }
 

Original file line number	Diff line number	Diff line change
`@@ -159,7 +159,7 @@ else if (_scatterGatherMethod == VariantProcessingStep.ScatterGatherMethod.fixed`
`159`	`159`
`160`	`160`	`public boolean doAllowSplitContigs()`
`161`	`161`	`{`
`162`		`- return getParameterJson().optBoolean("scatterGather.allowSplitChromosomes", true);`
	`162`	`+ return getParameterJson().optBoolean("scatterGather.allowSplitChromosomes", false);`
`163`	`163`	`}`
`164`	`164`
`165`	`165`	`public boolean isScatterJob()`
Original file line number	Diff line number	Diff line change
`@@ -248,7 +248,7 @@ private File runPbsvCall(JobContext ctx, List<File> inputs, ReferenceGenome geno`
`248`	`248`
`249`	`249`	`for (File s : inputs)`
`250`	`250`	`{`
`251`		`- String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' \| awk ' { $1 == \"" + contig + "\" } ' \| wc -l")));`
	`251`	`+ String ret = StringUtils.trimToNull(runner.executeWithOutput(Arrays.asList("/bin/bash", "-c", tabix.getExe().getPath() + " -l '" + s.getPath() + "' \| awk ' $1 == \"" + contig + "\" ' \| wc -l")));`
`252`	`252`	`if ("0".equals(ret))`
`253`	`253`	`{`
`254`	`254`	`ctx.getLogger().info("Sample is missing contig: " + contig + ", skipping: " + s.getPath());`
Original file line number	Diff line number	Diff line change
`@@ -64,6 +64,7 @@ savedFiles <- data.frame(datasetId = character(), datasetName = character(), fil`
`64`	`64`	`if (file.exists('/work/savedSeuratObjects.txt')) {`
`65`	`65`	`unlink('/work/savedSeuratObjects.txt')`
`66`	`66`	`}`
	`67`	`+file.create('/work/savedSeuratObjects.txt')`
`67`	`68`
`68`	`69`	`saveData <- function(seuratObj, datasetId) {`
`69`	`70`	`print(paste0('Saving dataset: ', datasetId))`
Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep`
`20`	`20`	`public Provider()`
`21`	`21`	`{`
`22`	`22`	`super("CiteSeqPlots", "CiteSeq/ADT Plots", "CellMembrane/Seurat", "This will create FeaturePlots for all features in the ADT assay.", Arrays.asList(`
`23`		`- SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{`
	`23`	`+ SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textfield", new JSONObject(){{`
`24`	`24`
`25`	`25`	`}}, "ADT")`
`26`	`26`	`), null, null);`