Ensure cellranger-dependent steps retain BAM

Author: bbimber

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

@@ -36,7 +36,6 @@ protected File runCellRanger(AlignmentOutputImpl output, Readset rs, List<File>
         File localBam = new File(outputDirectory, basename + ".cellranger.bam");
         File localBamIdx = SequenceAnalysisService.get().getExpectedBamOrCramIndex(localBam);
 
-
         String idParam = StringUtils.trimToNull(getProvider().getParameterByName("id").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));
         File cellrangerOutdir = new File(outputDirectory, CellRangerWrapper.getId(idParam, rs));
 

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

@@ -319,6 +319,18 @@ public boolean canAlignMultiplePairsAtOnce()
         return true;
     }
 
+    private boolean shouldDiscardBam()
+    {
+        return !_alwaysRetainBam &&  getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+    }
+
+    private boolean _alwaysRetainBam = false;
+
+    public void setAlwaysRetainBam(boolean alwaysRetainBam)
+    {
+        _alwaysRetainBam = alwaysRetainBam;
+    }
+
     @Override
     public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
     {
@@ -359,8 +371,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
         File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
         args.add("--transcriptome=" + indexDir.getPath());
 
-        boolean discardBam = getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
-        args.add("--create-bam=" + !discardBam);
+        args.add("--create-bam=" + !shouldDiscardBam());
 
         getWrapper().setWorkingDir(outputDirectory);
 
@@ -377,7 +388,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
         File outdir = new File(outputDirectory, id);
         outdir = new File(outdir, "outs");
 
-        if (!discardBam)
+        if (!shouldDiscardBam())
         {
             File bam = new File(outdir, "possorted_genome_bam.bam");
             if (!bam.exists())

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

@@ -67,6 +67,10 @@ public static List<ToolParameterDescriptor> getToolParameters()
     public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
     {
         AlignmentOutputImpl output = new AlignmentOutputImpl();
+
+        // We need to ensure we keep the BAM for post-processing:
+        setAlwaysRetainBam(true);
+
         File localBam = runCellRanger(output, rs, inputFastqs1, inputFastqs2, outputDirectory, referenceGenome, basename, readGroupId, platformUnit);
 
         File crDir = new File(localBam.getPath().replace(".nimble.cellranger.bam", ""));

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

@@ -67,6 +67,9 @@ public AlignmentStep create(PipelineContext context)
     public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
     {
         AlignmentOutputImpl output = new AlignmentOutputImpl();
+
+        setAlwaysRetainBam(true);
+
         File localBam = runCellRanger(output, rs, inputFastqs1, inputFastqs2, outputDirectory, referenceGenome, basename, readGroupId, platformUnit);
 
         File gtf = getPipelineCtx().getSequenceSupport().getCachedData(getProvider().getParameterByName("gtfFile").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class));