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Merge discvr-24.7 to discvr-24.11 #308

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Merged
bbimber merged 4 commits into from
Dec 6, 2024
Merged

Merge discvr-24.7 to discvr-24.11 #308

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e75375f
Make nimble output gzipped results file
bbimber Dec 5, 2024
ad8f951
Fix error in cell hashing
bbimber Dec 5, 2024
68205ae
Fix case in Sys.getenv()
bbimber Dec 5, 2024
c959503
Merge discvr-24.7 to discvr-24.11
bbimber Dec 6, 2024
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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/AppendMetadata.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/AppendNimble.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/AppendTcr.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/AvgExpression.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/ClassifyTNKByExpression.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/RunConga.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/StudyMetadata.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/resources/chunks/SummarizeTCellActivation.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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2 changes: 1 addition & 1 deletion singlecell/resources/chunks/TrainCelltypist.R
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Expand Up @@ -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'))
4 changes: 2 additions & 2 deletions singlecell/resources/chunks/UpdateSeuratPrototype.R
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Original file line number Diff line number Diff line change
@@ -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))
}

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4 changes: 2 additions & 2 deletions singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java
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Expand Up @@ -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;
Expand All @@ -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;
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4 changes: 3 additions & 1 deletion singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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());
}
}
Expand Down Expand Up @@ -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();
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