From 6382513e9c87b095a8b8b640795cf067ce5e3e5c Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 20 Dec 2023 09:27:26 -0800
Subject: [PATCH] Add memory argument to nimble

---
 singlecell/src/org/labkey/singlecell/run/NimbleHelper.java | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
index 99274666b..f8b1133ee 100644
--- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
+++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -451,6 +451,13 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         alignArgs.add("--input");
         alignArgs.add("/work/" + localBam.getName());
 
+        Integer maxRam = SequencePipelineService.get().getMaxRam();
+        if (maxRam != null)
+        {
+            alignArgs.add("-m");
+            alignArgs.add(maxRam + "000"); // in MB
+        }
+
         boolean dockerRan = runUsingDocker(alignArgs, output, "align.all");
         for (NimbleGenome genome : genomes)
         {