Merge pull request #308 from BimberLab/24.11_fb_merge

bbimber · web-flow · commit fb4d4c364b63 · 2024-12-06T10:16:24.000-08:00
Merge discvr-24.7 to discvr-24.11
diff --git a/singlecell/resources/chunks/AppendMetadata.R b/singlecell/resources/chunks/AppendMetadata.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/AppendNimble.R b/singlecell/resources/chunks/AppendNimble.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-  print(list.files(Sys.getEnv('USER_HOME')))
+  print(list.files(Sys.getenv('USER_HOME')))
   stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/AppendTcr.R b/singlecell/resources/chunks/AppendTcr.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/AvgExpression.R b/singlecell/resources/chunks/AvgExpression.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/ClassifyTNKByExpression.R b/singlecell/resources/chunks/ClassifyTNKByExpression.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/RunConga.R b/singlecell/resources/chunks/RunConga.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/StudyMetadata.R b/singlecell/resources/chunks/StudyMetadata.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/SummarizeTCellActivation.R b/singlecell/resources/chunks/SummarizeTCellActivation.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-    print(list.files(Sys.getEnv('USER_HOME')))
+    print(list.files(Sys.getenv('USER_HOME')))
     stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/resources/chunks/TrainCelltypist.R b/singlecell/resources/chunks/TrainCelltypist.R
@@ -6,4 +6,4 @@ datasetId <- names(seuratObjects)[[1]]
 printName(datasetId)
 seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-RIRA::TrainCellTypist(seuratObj, labelField = labelField, minCellsPerClass = minCellsPerClass, excludedClasses = excludedClasses, modelFile = modelFile, featureInclusionList = featureInclusionList, featureExclusionList = featureExclusionList, tempFileLocation = Sys.getEnv('WORK_DIR'))
+RIRA::TrainCellTypist(seuratObj, labelField = labelField, minCellsPerClass = minCellsPerClass, excludedClasses = excludedClasses, modelFile = modelFile, featureInclusionList = featureInclusionList, featureExclusionList = featureExclusionList, tempFileLocation = Sys.getenv('WORK_DIR'))
diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R
@@ -1,6 +1,6 @@
-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
 if (!file.exists(netRc)) {
-  print(list.files(Sys.getEnv('USER_HOME')))
+  print(list.files(Sys.getenv('USER_HOME')))
   stop(paste0('Unable to find file: ', netRc))
 }
 
diff --git a/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java b/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java
@@ -1234,7 +1234,7 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
             String allowableBarcodeParam = allowableBarcodes != null ? "c('" + StringUtils.join(allowableBarcodes, "','") + "')" : "NULL";
 
             List<String> methodNames = parameters.methods.stream().filter(m -> {
-                if (totalCellBarcodes > m.getMinCells())
+                if (totalCellBarcodes < m.getMinCells())
                 {
                     ctx.getLogger().debug("Dropping method due to insufficient cells: " + m.name());
                     return false;
@@ -1244,7 +1244,7 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
             }).map(CALLING_METHOD::getLabel).distinct().toList();
 
             List<String> consensusMethodNames = parameters.consensusMethods == null ? Collections.emptyList() : parameters.consensusMethods.stream().filter(m -> {
-                if (totalCellBarcodes > m.getMinCells())
+                if (totalCellBarcodes < m.getMinCells())
                 {
                     ctx.getLogger().debug("Dropping consensus method due to insufficient cells: " + m.name());
                     return false;
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -297,6 +297,8 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin
             {
                 if (SequencePipelineService.get().hasMinLineCount(results, 2))
                 {
+                    long lineCount = SequencePipelineService.get().getLineCount(results);
+                    _ctx.getLogger().debug("Found {} lines in file {}", lineCount, results.getPath());
                     throw new PipelineJobException("Unable to find file: " + reportHtml.getPath());
                 }
             }
@@ -496,7 +498,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
         reportArgs.add("-i");
         reportArgs.add(alignResultsGz.getPath());
 
-        File reportResultsGz = new File(ctx.getWorkingDirectory(), "reportResults." + genomeId + ".txt");
+        File reportResultsGz = new File(ctx.getWorkingDirectory(), "reportResults." + genomeId + ".txt.gz");
         if (reportResultsGz.exists())
         {
             reportResultsGz.delete();

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`		`-netRc <- paste0(Sys.getEnv('USER_HOME'), '/.netrc')`
	`1`	`+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')`
`2`	`2`	`if (!file.exists(netRc)) {`
`3`		`- print(list.files(Sys.getEnv('USER_HOME')))`
	`3`	`+ print(list.files(Sys.getenv('USER_HOME')))`
`4`	`4`	`stop(paste0('Unable to find file: ', netRc))`
`5`	`5`	`}`
`6`	`6`