add create bam option for new version

mskcc · Apr 2, 2024 · 18325f9 · 18325f9
1 parent a1ab25e
commit 18325f9
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/cellranger_config.py b/scripts/cellranger_config.py
@@ -58,7 +58,7 @@
 }
 
 # cellranger command line options
-OPTIONS = " --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200"
+OPTIONS = " --create-bam=true --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200"
 
 # 10X recipe list for different pipelines
 COUNT_FLAVORS = ["10X_Genomics_GeneExpression-3", "10X_Genomics_GeneExpression-5"]