From 3c500f7c1b68d19c7fab4f250b1c306ace1db7b3 Mon Sep 17 00:00:00 2001
From: RoriCremer <6863459+RoriCremer@users.noreply.github.com>
Date: Mon, 18 Apr 2022 22:21:51 -0400
Subject: [PATCH] correct auth in split intervals (#7790)

* correct auth in split intervals

* I dont like it, but at least we know it works
---
 scripts/variantstore/wdl/GvsUtils.wdl | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
index 779d5c56b84..5128b244f8b 100644
--- a/scripts/variantstore/wdl/GvsUtils.wdl
+++ b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -100,12 +100,6 @@ task SplitIntervals {
     set -e
     export GATK_LOCAL_JAR=~{default="/root/gatk.jar" gatk_override}
 
-    if [ ~{has_service_account_file} = 'true' ]; then
-      gsutil cp ~{service_account_json_path} local.service_account.json
-      export GOOGLE_APPLICATION_CREDENTIALS=local.service_account.json
-      gcloud auth activate-service-account --key-file=local.service_account.json
-    fi
-
     mkdir interval-files
     gatk --java-options "-Xmx~{java_memory}g" ~{gatkTool} \
       --dont-mix-contigs \
@@ -121,6 +115,11 @@ task SplitIntervals {
     # Drop trailing slash if one exists
     OUTPUT_GCS_DIR=$(echo ~{output_gcs_dir} | sed 's/\/$//')
 
+    if [ ~{has_service_account_file} = 'true' ]; then
+      gsutil cp ~{service_account_json_path} local.service_account.json
+      gcloud auth activate-service-account --key-file=local.service_account.json
+    fi
+
     if [ -n "$OUTPUT_GCS_DIR" ]; then
       gsutil -m cp *.interval_list $OUTPUT_GCS_DIR/
     fi