Update defaults for velocyto/samtools threads

bbimber · bbimber · commit 1998182cf2c1 · 2022-03-29T13:36:20.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/run/VelocytoAlignmentStep.java b/singlecell/src/org/labkey/singlecell/run/VelocytoAlignmentStep.java
@@ -169,10 +169,11 @@ public File runVelocytoFor10x(File localBam, File gtf, File outputFolder, @Nulla
             args.add(barcodeCSV.getPath());
 
             Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());
-            if (threads != null && threads > 1)
+            if (threads != null && threads >= 4)
             {
                 args.add("--samtools-threads");
-                args.add(String.valueOf(threads - 1));
+                // Cap this at 4 due to memory
+                args.add(String.valueOf(Math.min(threads - 2, 4)));
             }
 
             if (samtoolsMem != null)

Original file line number	Diff line number	Diff line change
`@@ -169,10 +169,11 @@ public File runVelocytoFor10x(File localBam, File gtf, File outputFolder, @Nulla`
`169`	`169`	`args.add(barcodeCSV.getPath());`
`170`	`170`
`171`	`171`	`Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());`
`172`		`- if (threads != null && threads > 1)`
	`172`	`+ if (threads != null && threads >= 4)`
`173`	`173`	`{`
`174`	`174`	`args.add("--samtools-threads");`
`175`		`- args.add(String.valueOf(threads - 1));`
	`175`	`+ // Cap this at 4 due to memory`
	`176`	`+ args.add(String.valueOf(Math.min(threads - 2, 4)));`
`176`	`177`	`}`
`177`	`178`
`178`	`179`	`if (samtoolsMem != null)`