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Allow CellRanger to more easily skip BAM creation
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@bbimber
bbimber committed Aug 25, 2024
1 parent 7008b39 commit 4b3375e
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Showing 2 changed files with 56 additions and 44 deletions.
89 changes: 49 additions & 40 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1383,57 +1383,66 @@ public File doAlignmentForSet(List<Pair<File, File>> inputFiles, ReferenceGenome
AlignmentStep.AlignmentOutput alignmentOutput = alignmentStep.performAlignment(rs, forwardFastqs, reverseFastqs, outputDirectory, referenceGenome, SequenceTaskHelper.getUnzippedBaseName(inputFiles.get(0).first.getName()) + "." + alignmentStep.getProvider().getName().toLowerCase(), String.valueOf(lowestReadDataId), platformUnit);
getHelper().getFileManager().addStepOutputs(alignmentAction, alignmentOutput);

if (alignmentOutput.getBAM() == null || !alignmentOutput.getBAM().exists())
{
throw new PipelineJobException("Unable to find BAM file after alignment: " + alignmentOutput.getBAM());
}
Date end = new Date();
alignmentAction.setEndTime(end);
getJob().getLogger().info(alignmentStep.getProvider().getLabel() + " Duration: " + DurationFormatUtils.formatDurationWords(end.getTime() - start.getTime(), true, true));
actions.add(alignmentAction);

SequenceUtil.logFastqBamDifferences(getJob().getLogger(), alignmentOutput.getBAM());

ToolParameterDescriptor mergeParam = alignmentStep.getProvider().getParameterByName(AbstractAlignmentStepProvider.SUPPORT_MERGED_UNALIGNED);
boolean doMergeUnaligned = alignmentStep.getProvider().supportsMergeUnaligned() && mergeParam != null && mergeParam.extractValue(getJob(), alignmentStep.getProvider(), alignmentStep.getStepIdx(), Boolean.class, false);
if (doMergeUnaligned)
boolean discardBam = alignmentStep.getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getJob(), alignmentStep.getProvider(), alignmentStep.getStepIdx(), Boolean.class, false);
if (discardBam && alignmentOutput.getBAM() == null)
{
getJob().setStatus(PipelineJob.TaskStatus.running, "MERGING UNALIGNED READS INTO BAM" + msgSuffix);
getJob().getLogger().info("merging unaligned reads into BAM");
File idx = SequenceAnalysisService.get().getExpectedBamOrCramIndex(alignmentOutput.getBAM());
if (idx.exists())
{
getJob().getLogger().debug("deleting index: " + idx.getPath());
idx.delete();
}

//merge unaligned reads and clean file
MergeBamAlignmentWrapper wrapper = new MergeBamAlignmentWrapper(getJob().getLogger());
wrapper.executeCommand(referenceGenome.getWorkingFastaFile(), alignmentOutput.getBAM(), inputFiles, null);
getHelper().getFileManager().addCommandsToAction(wrapper.getCommandsExecuted(), alignmentAction);
getJob().getLogger().info("The alignment did not produce a BAM, but discardBam was selected. BAM stats steps will be skipped.");
}
else
{
getJob().getLogger().info("skipping merge of unaligned reads on BAM");
}
if (alignmentOutput.getBAM() == null || !alignmentOutput.getBAM().exists())
{
throw new PipelineJobException("Unable to find BAM file after alignment: " + alignmentOutput.getBAM());
}

if (alignmentStep.doAddReadGroups())
{
getJob().setStatus(PipelineJob.TaskStatus.running, "ADDING READ GROUPS" + msgSuffix);
AddOrReplaceReadGroupsWrapper wrapper = new AddOrReplaceReadGroupsWrapper(getJob().getLogger());
wrapper.executeCommand(alignmentOutput.getBAM(), null, rs.getReadsetId().toString(), rs.getPlatform(), (platformUnit == null ? rs.getReadsetId().toString() : platformUnit), rs.getName().replaceAll(" ", "_"));
getHelper().getFileManager().addCommandsToAction(wrapper.getCommandsExecuted(), alignmentAction);
}
else
{
getJob().getLogger().info("skipping read group assignment");
}
SequenceUtil.logFastqBamDifferences(getJob().getLogger(), alignmentOutput.getBAM());

//generate stats
getJob().setStatus(PipelineJob.TaskStatus.running, "Generating BAM Stats");
FlagStatRunner runner = new FlagStatRunner(getJob().getLogger());
runner.execute(alignmentOutput.getBAM());
getHelper().getFileManager().addCommandsToAction(runner.getCommandsExecuted(), alignmentAction);
ToolParameterDescriptor mergeParam = alignmentStep.getProvider().getParameterByName(AbstractAlignmentStepProvider.SUPPORT_MERGED_UNALIGNED);
boolean doMergeUnaligned = alignmentStep.getProvider().supportsMergeUnaligned() && mergeParam != null && mergeParam.extractValue(getJob(), alignmentStep.getProvider(), alignmentStep.getStepIdx(), Boolean.class, false);
if (doMergeUnaligned)
{
getJob().setStatus(PipelineJob.TaskStatus.running, "MERGING UNALIGNED READS INTO BAM" + msgSuffix);
getJob().getLogger().info("merging unaligned reads into BAM");
File idx = SequenceAnalysisService.get().getExpectedBamOrCramIndex(alignmentOutput.getBAM());
if (idx.exists())
{
getJob().getLogger().debug("deleting index: " + idx.getPath());
idx.delete();
}

//merge unaligned reads and clean file
MergeBamAlignmentWrapper wrapper = new MergeBamAlignmentWrapper(getJob().getLogger());
wrapper.executeCommand(referenceGenome.getWorkingFastaFile(), alignmentOutput.getBAM(), inputFiles, null);
getHelper().getFileManager().addCommandsToAction(wrapper.getCommandsExecuted(), alignmentAction);
}
else
{
getJob().getLogger().info("skipping merge of unaligned reads on BAM");
}

if (alignmentStep.doAddReadGroups())
{
getJob().setStatus(PipelineJob.TaskStatus.running, "ADDING READ GROUPS" + msgSuffix);
AddOrReplaceReadGroupsWrapper wrapper = new AddOrReplaceReadGroupsWrapper(getJob().getLogger());
wrapper.executeCommand(alignmentOutput.getBAM(), null, rs.getReadsetId().toString(), rs.getPlatform(), (platformUnit == null ? rs.getReadsetId().toString() : platformUnit), rs.getName().replaceAll(" ", "_"));
getHelper().getFileManager().addCommandsToAction(wrapper.getCommandsExecuted(), alignmentAction);
}
else
{
getJob().getLogger().info("skipping read group assignment");
}

//generate stats
getJob().setStatus(PipelineJob.TaskStatus.running, "Generating BAM Stats");
FlagStatRunner runner = new FlagStatRunner(getJob().getLogger());
runner.execute(alignmentOutput.getBAM());
getHelper().getFileManager().addCommandsToAction(runner.getCommandsExecuted(), alignmentAction);
}

_resumer.setReadDataAlignmentDone(lowestReadDataId, actions, alignmentOutput.getBAM());

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11 changes: 7 additions & 4 deletions singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java
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Original file line number Diff line number Diff line change
Expand Up @@ -377,12 +377,15 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
File outdir = new File(outputDirectory, id);
outdir = new File(outdir, "outs");

File bam = new File(outdir, "possorted_genome_bam.bam");
if (!bam.exists())
if (!discardBam)
{
throw new PipelineJobException("Unable to find file: " + bam.getPath());
File bam = new File(outdir, "possorted_genome_bam.bam");
if (!bam.exists())
{
throw new PipelineJobException("Unable to find file: " + bam.getPath());
}
output.setBAM(bam);
}
output.setBAM(bam);

getWrapper().deleteSymlinks(getWrapper().getLocalFastqDir(outputDirectory));

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