From aa49aac0fc0df82f2646273699a6d7003fa50b60 Mon Sep 17 00:00:00 2001
From: Yixiao <gongyixiao@gmail.com>
Date: Fri, 21 Jan 2022 21:50:09 -0500
Subject: [PATCH] change oncokb url

---
 conf/singularity.config | 2 +-
 pipeline.nf             | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/singularity.config b/conf/singularity.config
index 469d9c565..10d373848 100644
--- a/conf/singularity.config
+++ b/conf/singularity.config
@@ -9,7 +9,7 @@
 singularity {
     enabled = true
     autoMounts = true
-    runOptions = "-B $TMPDIR"
+    runOptions = "-e --no-home -B $TMPDIR"
 }
 
 process {
diff --git a/pipeline.nf b/pipeline.nf
index 4a5756724..1a37a65a0 100755
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -1472,6 +1472,7 @@ process SomaticAnnotateMaf {
     --filter-vcf 0
     
   python /usr/bin/oncokb_annotator/MafAnnotator.py \
+    -u "https://legacy.oncokb.org/api/v1" \
     -i ${outputPrefix}.raw.maf \
     -o ${outputPrefix}.raw.oncokb.maf