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Support --skip-tso-trimming nimble flag
1 parent 8dad895 commit 509f6bb

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4 files changed

+29
-51
lines changed

4 files changed

+29
-51
lines changed

‎singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -89,19 +89,22 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
8989
File loupeFile = getCachedLoupeFile(rs, throwIfNotFound);
9090

9191
File localBam;
92+
boolean skipTsoTrimming;
9293
if (loupeFile == null)
9394
{
9495
localBam = performCellRangerAlignment(output, rs, inputFastqs1, inputFastqs2, outputDirectory, referenceGenome, basename, readGroupId, platformUnit);
96+
skipTsoTrimming = false;
9597
}
9698
else
9799
{
98100
localBam = createNimbleBam(output, rs, inputFastqs1, inputFastqs2);
101+
skipTsoTrimming = true;
99102
}
100103

101104

102105
// Now run nimble itself:
103106
NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
104-
helper.doNimbleAlign(localBam, output, rs, basename);
107+
helper.doNimbleAlign(localBam, output, rs, basename, skipTsoTrimming);
105108
output.setBAM(localBam);
106109

107110
return output;

‎singlecell/src/org/labkey/singlecell/run/NimbleAnalysis.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
5656
{
5757
AnalysisOutputImpl output = new AnalysisOutputImpl();
5858
NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
59-
helper.doNimbleAlign(inputBam, output, rs, FileUtil.getBaseName(inputBam));
59+
helper.doNimbleAlign(inputBam, output, rs, FileUtil.getBaseName(inputBam), false);
6060

6161
return output;
6262
}

‎singlecell/src/org/labkey/singlecell/run/NimbleBulkAlignmentStep.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -144,7 +144,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
144144

145145
// Now run nimble itself:
146146
NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
147-
helper.doNimbleAlign(outputBam, output, rs, basename);
147+
helper.doNimbleAlign(outputBam, output, rs, basename, true);
148148
output.setBAM(outputBam);
149149

150150
return output;

‎singlecell/src/org/labkey/singlecell/run/NimbleHelper.java‎

Lines changed: 23 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -162,7 +162,7 @@ public void prepareGenome(int genomeId) throws PipelineJobException
162162

163163
private File getLocalIndexDir(int genomeId, boolean createIfMissing)
164164
{
165-
File dir = new File(getPipelineCtx().getSourceDirectory(), "genome." + genomeId);
165+
File dir = FileUtil.appendName(getPipelineCtx().getSourceDirectory(), "genome." + genomeId);
166166
if (createIfMissing && !dir.exists())
167167
{
168168
dir.mkdir();
@@ -187,10 +187,10 @@ private File getGenomeCsv(int genomeId, boolean forceWorkDir) throws PipelineJob
187187
if (!forceWorkDir && AlignerIndexUtil.hasCachedIndex(getPipelineCtx(), "nimble", rg))
188188
{
189189
File indexDir = AlignerIndexUtil.getIndexDir(rg, "nimble");
190-
return new File(indexDir, "genome." + genomeId + ".csv");
190+
return FileUtil.appendName(indexDir, "genome." + genomeId + ".csv");
191191
}
192192

193-
return checkForLegacyGenome(new File(getLocalIndexDir(genomeId, true), "genome." + genomeId + ".csv"));
193+
return FileUtil.appendName(getLocalIndexDir(genomeId, true), "genome." + genomeId + ".csv");
194194
}
195195

196196
private File getGenomeFasta(int genomeId) throws PipelineJobException
@@ -209,43 +209,13 @@ private File getGenomeFasta(int genomeId, boolean forceWorkDir) throws PipelineJ
209209
if (!forceWorkDir && AlignerIndexUtil.hasCachedIndex(getPipelineCtx(), "nimble", rg))
210210
{
211211
File indexDir = AlignerIndexUtil.getIndexDir(rg, "nimble");
212-
return new File(indexDir, "genome." + genomeId + ".fasta");
212+
return FileUtil.appendName(indexDir, "genome." + genomeId + ".fasta");
213213
}
214214

215-
return checkForLegacyGenome(new File(getLocalIndexDir(genomeId, true), "genome." + genomeId + ".fasta"));
215+
return FileUtil.appendName(getLocalIndexDir(genomeId, true), "genome." + genomeId + ".fasta");
216216
}
217217

218-
// TODO: This should ultimately be removed:
219-
private File checkForLegacyGenome(File fileNewLocation) throws PipelineJobException
220-
{
221-
if (fileNewLocation.exists())
222-
{
223-
return fileNewLocation;
224-
}
225-
226-
File oldLocation = new File(fileNewLocation.getParentFile().getParentFile(), fileNewLocation.getName());
227-
if (oldLocation.exists())
228-
{
229-
getPipelineCtx().getLogger().debug("Genome file found in old location, moving: " + oldLocation.getPath());
230-
if (!fileNewLocation.getParentFile().exists())
231-
{
232-
fileNewLocation.getParentFile().mkdir();
233-
}
234-
235-
try
236-
{
237-
FileUtils.moveFile(oldLocation, fileNewLocation);
238-
}
239-
catch (IOException e)
240-
{
241-
throw new PipelineJobException(e);
242-
}
243-
}
244-
245-
return fileNewLocation;
246-
}
247-
248-
public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, String basename) throws UnsupportedOperationException, PipelineJobException
218+
public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, String basename, boolean doTsoTrimming) throws UnsupportedOperationException, PipelineJobException
249219
{
250220
getPipelineCtx().getJob().setStatus(PipelineJob.TaskStatus.running, "Running Nimble Align");
251221
List<NimbleGenome> genomes = getGenomes();
@@ -274,7 +244,7 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin
274244
jsons.add(refJson);
275245
}
276246

277-
Map<NimbleGenome, File> resultMap = doAlignment(genomes, jsons, bam, output);
247+
Map<NimbleGenome, File> resultMap = doAlignment(genomes, jsons, bam, output, doTsoTrimming);
278248
for (NimbleGenome genome : genomes)
279249
{
280250
File results = resultMap.get(genome);
@@ -307,7 +277,7 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin
307277

308278
private File prepareReference(File genomeCsv, File genomeFasta, NimbleGenome genome, PipelineStepOutput output) throws PipelineJobException
309279
{
310-
File nimbleJson = new File(getPipelineCtx().getWorkingDirectory(), genome.genomeId + ".json");
280+
File nimbleJson = FileUtil.appendName(getPipelineCtx().getWorkingDirectory(), genome.genomeId + ".json");
311281
runUsingDocker(Arrays.asList("python3", "-m", "nimble", "generate", "--opt-file", genomeFasta.getPath(), "--file", genomeCsv.getPath(), "--output_path", nimbleJson.getPath()), output, "generate-" + genome.genomeId);
312282
if (!nimbleJson.exists())
313283
{
@@ -401,7 +371,7 @@ else if ("strict".equals(alignTemplate))
401371
}
402372
}
403373

404-
private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<File> refJsons, File bam, PipelineStepOutput output) throws PipelineJobException
374+
private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<File> refJsons, File bam, PipelineStepOutput output, boolean skipTsoTrimming) throws PipelineJobException
405375
{
406376
Map<NimbleGenome, File> resultMap = new HashMap<>();
407377

@@ -425,7 +395,12 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
425395
alignArgs.add(strandedness);
426396
}
427397

428-
File alignmentTsvBase = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + (genomes.size() == 1 ? genomes.get(0).genomeId + "." : "") + "txt.gz");
398+
if (skipTsoTrimming)
399+
{
400+
alignArgs.add("--skip_tso_trimming");
401+
}
402+
403+
File alignmentTsvBase = FileUtil.appendName(getPipelineCtx().getWorkingDirectory(), "alignResults." + (genomes.size() == 1 ? genomes.get(0).genomeId + "." : "") + "txt.gz");
429404

430405
alignArgs.add("--reference");
431406
alignArgs.add(refJsons.stream().map(File::getPath).collect(Collectors.joining(",")));
@@ -437,7 +412,7 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
437412
alignArgs.add(bam.getPath());
438413

439414
// Create temp folder:
440-
File tmpDir = new File(getPipelineCtx().getWorkingDirectory(), "tmpDir");
415+
File tmpDir = FileUtil.appendName(getPipelineCtx().getWorkingDirectory(), "tmpDir");
441416
if (tmpDir.exists())
442417
{
443418
try
@@ -473,7 +448,7 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
473448

474449
for (NimbleGenome genome : genomes)
475450
{
476-
File alignResultsGz = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + genome.genomeId + ".txt.gz");
451+
File alignResultsGz = FileUtil.appendName(getPipelineCtx().getWorkingDirectory(), "alignResults." + genome.genomeId + ".txt.gz");
477452
if (dockerRan && !alignResultsGz.exists())
478453
{
479454
File doneFile = getNimbleDoneFile(getPipelineCtx().getWorkingDirectory(), "align.all");
@@ -508,7 +483,7 @@ public static void write10xBarcodes(File bam, Logger log, Readset rs, ReferenceG
508483
barcodeArgs.add("-I");
509484
barcodeArgs.add(bam.getPath());
510485

511-
File bcOutput = new File(bam.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(bam.getName()) + ".cb.txt.gz");
486+
File bcOutput = FileUtil.appendName(bam.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(bam.getName()) + ".cb.txt.gz");
512487
barcodeArgs.add("--output");
513488
barcodeArgs.add(bcOutput.getPath());
514489

@@ -531,7 +506,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
531506
String resumeString = "nimble.report." + genomeId;
532507
File doneFile = getNimbleDoneFile(ctx.getWorkingDirectory(), resumeString);
533508

534-
File reportResultsGz = new File(ctx.getWorkingDirectory(), "reportResults." + genomeId + ".txt.gz");
509+
File reportResultsGz = FileUtil.appendName(ctx.getWorkingDirectory(), "reportResults." + genomeId + ".txt.gz");
535510
if (reportResultsGz.exists() && !doneFile.exists())
536511
{
537512
ctx.getLogger().debug("Deleting existing result file: " + reportResultsGz.getPath());
@@ -591,7 +566,7 @@ public static File getReportHtmlFileFromResults(File reportResults)
591566

592567
private static File getNimbleDoneFile(File parentDir, String resumeString)
593568
{
594-
return new File(parentDir, "nimble." + resumeString + ".done");
569+
return FileUtil.appendName(parentDir, "nimble." + resumeString + ".done");
595570
}
596571

597572
public static File runFastqToBam(PipelineStepOutput output, PipelineContext ctx, Readset rs, List<File> inputFastqs1, List<File> inputFastqs2, File loupeFile) throws PipelineJobException
@@ -600,7 +575,7 @@ public static File runFastqToBam(PipelineStepOutput output, PipelineContext ctx,
600575
int bamIdx = 0;
601576
while (bamIdx < inputFastqs1.size())
602577
{
603-
File outputBam = new File(ctx.getWorkingDirectory(), FileUtil.makeLegalName(rs.getName()) + ".unmapped." + bamIdx + ".bam");
578+
File outputBam = FileUtil.appendName(ctx.getWorkingDirectory(), FileUtil.makeLegalName(rs.getName()) + ".unmapped." + bamIdx + ".bam");
604579

605580
List<String> args = new ArrayList<>();
606581
args.add("python3");
@@ -641,7 +616,7 @@ public static File runFastqToBam(PipelineStepOutput output, PipelineContext ctx,
641616
File outputBam;
642617
if (outputBams.size() > 1)
643618
{
644-
outputBam = new File(ctx.getWorkingDirectory(), FileUtil.makeLegalName(rs.getName()) + ".unmapped.bam");
619+
outputBam = FileUtil.appendName(ctx.getWorkingDirectory(), FileUtil.makeLegalName(rs.getName()) + ".unmapped.bam");
645620
outputBams.forEach(output::addIntermediateFile);
646621

647622
SamtoolsRunner st = new SamtoolsRunner(ctx.getLogger());
@@ -777,7 +752,7 @@ private String getVersion(PipelineStepOutput output) throws PipelineJobException
777752

778753
runUsingDocker(nimbleArgs, output, null);
779754

780-
File outFile = new File(getPipelineCtx().getWorkingDirectory(), "nimbleVersion.txt");
755+
File outFile = FileUtil.appendName(getPipelineCtx().getWorkingDirectory(), "nimbleVersion.txt");
781756
if (!outFile.exists())
782757
{
783758
throw new PipelineJobException("Unable to find file: " + outFile.getPath());

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