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Bugfix when cell hashing and CITE-seq used together for Seurat
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5 files changed

+61
-14
lines changed

5 files changed

+61
-14
lines changed

‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -124,5 +124,5 @@ static public void setInstance(SequencePipelineService instance)
124124

125125
abstract public PreprocessingStep.Output simpleTrimFastqPair(File fq1, File fq2, List<String> params, File outDir, Logger log) throws PipelineJobException;
126126

127-
abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls) throws PipelineJobException;
127+
abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls, boolean createOutputFiles) throws PipelineJobException;
128128
}

‎SequenceAnalysis/resources/external/scRNAseq/htoClassifier.Rmd‎

Lines changed: 10 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,4 +48,13 @@ if (nrow(barcodeData) > 0 && ncol(barcodeData) > 0){
4848
}
4949
}
5050
51-
```
51+
```
52+
53+
## Print Session Info
54+
55+
```{r SessionInfo}
56+
57+
sessionInfo()
58+
59+
```
60+

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -520,10 +520,10 @@ else if (!SequenceUtil.hasLineCount(f))
520520
}
521521

522522
@Override
523-
public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls) throws PipelineJobException
523+
public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls, boolean createOutputFiles) throws PipelineJobException
524524
{
525525
CellHashingHandler handler = new CellHashingHandler();
526526

527-
return handler.runCiteSeqCount(output, outputCategory, htoReadset, htoList, cellBarcodeList, outputDir, basename, log, extraArgs, doHtoFiltering, minCountPerCell, localPipelineDir, editDistance, scanEditDistances, parentReadset, genomeId, generateHtoCalls ? CellHashingHandler.BARCODE_TYPE.hashing : CellHashingHandler.BARCODE_TYPE.citeseq);
527+
return handler.runCiteSeqCount(output, outputCategory, htoReadset, htoList, cellBarcodeList, outputDir, basename, log, extraArgs, doHtoFiltering, minCountPerCell, localPipelineDir, editDistance, scanEditDistances, parentReadset, genomeId, generateHtoCalls ? CellHashingHandler.BARCODE_TYPE.hashing : CellHashingHandler.BARCODE_TYPE.citeseq, createOutputFiles);
528528
}
529529
}

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CellHashingHandler.java‎

Lines changed: 47 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -55,6 +55,7 @@
5555
import java.util.ArrayList;
5656
import java.util.Arrays;
5757
import java.util.HashMap;
58+
import java.util.HashSet;
5859
import java.util.List;
5960
import java.util.Map;
6061
import java.util.Set;
@@ -604,7 +605,7 @@ private Map<String, Object> parseUnknownBarcodes(File unknownBarcodeFile, File l
604605
return ret;
605606
}
606607

607-
private File ensureLocalCopy(File input, File outputDir, Logger log) throws PipelineJobException
608+
private File ensureLocalCopy(File input, File outputDir, Logger log, Set<File> toDelete) throws PipelineJobException
608609
{
609610
if (!outputDir.equals(input.getParentFile()))
610611
{
@@ -633,6 +634,9 @@ private File ensureLocalCopy(File input, File outputDir, Logger log) throws Pipe
633634
{
634635
FileUtils.copyFile(input, dest);
635636
}
637+
638+
toDelete.add(dest);
639+
636640
return dest;
637641
}
638642
catch (IOException e)
@@ -650,13 +654,15 @@ public File generateFinalCalls(File citeSeqCountOutDir, File outputDir, String b
650654

651655
String scriptWrapper = getScriptPath("sequenceanalysis", "/external/scRNAseq/htoClassifier.sh");
652656

657+
Set<File> toDelete = new HashSet<>();
658+
653659
SimpleScriptWrapper rWrapper = new SimpleScriptWrapper(log);
654660
rWrapper.setWorkingDir(outputDir);
655661

656-
citeSeqCountOutDir = ensureLocalCopy(citeSeqCountOutDir, outputDir, log);
662+
citeSeqCountOutDir = ensureLocalCopy(citeSeqCountOutDir, outputDir, log, toDelete);
657663
if (cellBarcodeWhitelist != null)
658664
{
659-
cellBarcodeWhitelist = ensureLocalCopy(cellBarcodeWhitelist, outputDir, log);
665+
cellBarcodeWhitelist = ensureLocalCopy(cellBarcodeWhitelist, outputDir, log, toDelete);
660666
}
661667

662668
File rScript = new File(getScriptPath("sequenceanalysis", "/external/scRNAseq/htoClassifier.Rmd"));
@@ -707,6 +713,26 @@ public File generateFinalCalls(File citeSeqCountOutDir, File outputDir, String b
707713
throw new PipelineJobException("Unable to find HTO calls file: " + callsFile.getPath());
708714
}
709715

716+
try
717+
{
718+
for (File f : toDelete)
719+
{
720+
log.debug("deleting local copy: " + f.getPath());
721+
if (f.isDirectory())
722+
{
723+
FileUtils.deleteDirectory(f);
724+
}
725+
else
726+
{
727+
f.delete();
728+
}
729+
}
730+
}
731+
catch (IOException e)
732+
{
733+
throw new PipelineJobException(e);
734+
}
735+
710736
return callsFile;
711737
}
712738

@@ -830,12 +856,12 @@ private HtoMergeResult possiblyMergeHtoFastqs(Readset htoReadset, File outdir, L
830856
return ret;
831857
}
832858

833-
public File runCiteSeqCount(PipelineStepOutput output, String category, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, BARCODE_TYPE type) throws PipelineJobException
859+
public File runCiteSeqCount(PipelineStepOutput output, String category, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, BARCODE_TYPE type, boolean createOutputFiles) throws PipelineJobException
834860
{
835861
HtoMergeResult htoFastqs = possiblyMergeHtoFastqs(htoReadset, outputDir, log);
836862
if (!htoFastqs.intermediateFiles.isEmpty())
837863
{
838-
htoFastqs.intermediateFiles.forEach(x -> output.addIntermediateFile(x));
864+
htoFastqs.intermediateFiles.forEach(output::addIntermediateFile);
839865
}
840866

841867
if (scanEditDistances && !type.isSupportsScan())
@@ -915,8 +941,8 @@ public File runCiteSeqCount(PipelineStepOutput output, String category, Readset
915941
File unknownBarcodeFile = getCiteSeqCountUnknownOutput(localPipelineDir == null ? outputDir : localPipelineDir, type, ed);
916942
toolArgs.add(unknownBarcodeFile.getPath());
917943

918-
File citeSeqCountOutDir = new File(outputDir, basename + ".citeSeqCounts." + ed);
919-
String outputBasename = basename + "." + ed;
944+
File citeSeqCountOutDir = new File(outputDir, basename + ".citeSeqCounts." + ed + "." + type.name());
945+
String outputBasename = basename + "." + ed + "." + type.name();
920946
Map<String, Object> callMap = executeCiteSeqCountWithJobCtx(outputDir, outputBasename, citeSeqCountOutDir, htoFastqs.files.getLeft(), htoFastqs.files.getRight(), toolArgs, ed, log, cellBarcodeList, doHtoFiltering, minCountPerCell, localPipelineDir, unknownBarcodeFile, type);
921947
results.put(ed, callMap);
922948

@@ -978,11 +1004,15 @@ public File runCiteSeqCount(PipelineStepOutput output, String category, Readset
9781004
throw new PipelineJobException("html file was null");
9791005
}
9801006

981-
if (category != null)
1007+
if (createOutputFiles && category != null)
9821008
{
9831009
output.addSequenceOutput(htoCalls, parentReadset.getName() + ": Cell Hashing Calls", category, parentReadset.getReadsetId(), null, genomeId, description);
9841010
output.addSequenceOutput(html, parentReadset.getName() + ": Cell Hashing Report", category + ": Report", parentReadset.getReadsetId(), null, genomeId, description);
9851011
}
1012+
else
1013+
{
1014+
log.debug("Output files will not be created");
1015+
}
9861016

9871017
return htoCalls;
9881018
}
@@ -992,7 +1022,15 @@ public File runCiteSeqCount(PipelineStepOutput output, String category, Readset
9921022

9931023
String description = String.format("%% Mapped: %s\n%% Unmapped: %s", callMap.get("PercentageMapped"), callMap.get("PercentageUnmapped"));
9941024
File citeSeqCount = (File) callMap.get("citeSeqCountMatrix");
995-
output.addSequenceOutput(citeSeqCount, parentReadset.getName() + ": CITE-Seq Count Matrix", (category == null ? "CITE-Seq Count Matrix" : category), parentReadset.getReadsetId(), null, genomeId, description);
1025+
1026+
if (createOutputFiles)
1027+
{
1028+
output.addSequenceOutput(citeSeqCount, parentReadset.getName() + ": CITE-Seq Count Matrix", (category == null ? "CITE-Seq Count Matrix" : category), parentReadset.getReadsetId(), null, genomeId, description);
1029+
}
1030+
else
1031+
{
1032+
log.debug("Output files will not be created");
1033+
}
9961034

9971035
File outDir = (File) callMap.get("outputDir");
9981036
output.removeIntermediateFiles(outDir);

‎blast/src/org/labkey/blast/pipeline/BlastDatabasePipelineJob.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -117,7 +117,7 @@ private void possiblyCreateDbRecord()
117117

118118
TableInfo referenceLibraries = DbSchema.get(BLASTManager.SEQUENCE_ANALYSIS).getTable("reference_libraries");
119119
TableSelector ts = new TableSelector(referenceLibraries, PageFlowUtil.set("name", "description", "fasta_file"), new SimpleFilter(FieldKey.fromString("rowid"), getLibraryId()), null);
120-
Map<String, Object> libraryMap = ts.getObject(Map.class);
120+
Map<String, Object> libraryMap = ts.getMap();
121121
Integer dataId = (Integer)libraryMap.get("fasta_file");
122122
if (dataId == null)
123123
{

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