Use consistent name for nimbleStats file

bbimber · bbimber · commit c077fbc4e951 · 2023-01-07T11:27:31.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -297,7 +297,7 @@ private File doAlignment(NimbleGenome genome, File refJson, File bam, PipelineSt
         }
 
         alignArgs.add("-l");
-        alignArgs.add("/work/nimbleDebug." + genome.genomeId + ".txt");
+        alignArgs.add("/work/" + getNimbleLogFile(getPipelineCtx().getWorkingDirectory(), genome.genomeId).getName());
 
         boolean alignOutput = getProvider().getParameterByName(ALIGN_OUTPUT).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
         File alignmentOutputFile = new File(getPipelineCtx().getWorkingDirectory(), "nimbleAlignment." + genome.genomeId + ".txt.gz");

Original file line number	Diff line number	Diff line change
`@@ -297,7 +297,7 @@ private File doAlignment(NimbleGenome genome, File refJson, File bam, PipelineSt`
`297`	`297`	`}`
`298`	`298`
`299`	`299`	`alignArgs.add("-l");`
`300`		`- alignArgs.add("/work/nimbleDebug." + genome.genomeId + ".txt");`
	`300`	`+ alignArgs.add("/work/" + getNimbleLogFile(getPipelineCtx().getWorkingDirectory(), genome.genomeId).getName());`
`301`	`301`
`302`	`302`	`boolean alignOutput = getProvider().getParameterByName(ALIGN_OUTPUT).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);`
`303`	`303`	`File alignmentOutputFile = new File(getPipelineCtx().getWorkingDirectory(), "nimbleAlignment." + genome.genomeId + ".txt.gz");`