diff --git a/conf/singularity.config b/conf/singularity.config index 469d9c56..10d37384 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 4a575672..1a37a65a 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