change oncokb url

mskcc · Jan 22, 2022 · aa49aac · aa49aac
1 parent 830df8e
commit aa49aac
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diff --git 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
@@ -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