updated arguments list

icbi-lab · Mar 20, 2021 · 0ec4e8a · 0ec4e8a
1 parent 9d399e4
commit 0ec4e8a
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diff --git a/NeoFuse b/NeoFuse
@@ -87,7 +87,7 @@ if [ "$BUILD" == "false" ]; then
 	-T: Percentile rank threshold (default: Inf)
 	-c: Mimimum confidence score (H, M or L; default: L)
 	-C: Custom HLA I list (TXT file containing custom HLA I types)
-	-k: Keep STAR output
+	-k: Keep STAR output (BAM files)
 	-l: int>=0:  maximum available RAM (bytes) for sorting BAM
 
 	--singularity: NeoFuse will use the Singularity image

diff --git a/README.md b/README.md
@@ -118,6 +118,12 @@ $ NeoFuse <arguments> [options] --singularity (or --docker)
 
 **-c:** Mimimum confidence score (values: H, M, or L; default: L) **
 
+**-C:** Custom HLA I list (TXT file containing custom HLA I types) **
+
+**-k:** Keep STAR output (BAM files) **
+
+**-l:** int>=0:  maximum available RAM (bytes) for sorting BAM **
+
 **--singularity:** NeoFuse will use the Singularity image
 
 **--docker:** NeoFuse will use the Docker image
@@ -181,6 +187,12 @@ $ NeoFuse <arguments> [options] --singularity (or --docker)
 
 **-c:** Mimimum confidence score (values: H, M, or L; default: L) **
 
+**-C:** Custom HLA I list (TXT file containing custom HLA I types) **
+
+**-k:** Keep STAR output (BAM files) **
+
+**-l:** int>=0:  maximum available RAM (bytes) for sorting BAM **
+
 **--singularity:** NeoFuse will use the Singularity image
 
 **--docker:** NeoFuse will use the Docker image