Merge pull request #133 from wustl-oncology/varscan-somatic-compute

moved the set -o lines under the ACCESS_TOKEN block

definitions/tools/varscan_somatic.wdl

@@ -25,24 +25,27 @@ task varscanSomatic {
   runtime {
     preemptible: 1
     maxRetries: 2
+
     memory: "12GB"
     cpu: 2
     docker: "mgibio/varscan-cwl:v2.4.2-samtools1.16.1"
     disks: "local-disk ~{space_needed_gb} HDD"
   }
 
   command <<<
-    set -o errexit
-    set -o nounset
-    set -o pipefail
-
+
     ACCESS_TOKEN=$(wget -O - --header "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/service-accounts/default/token?alt=text 2> /dev/null | grep access_token)
     if [[ "$ACCESS_TOKEN" == "access_token"* ]]; then
        # When the BAMs aren't localized in GCP, samtools needs this token to access them via gs:// URLs.
        export GCS_OAUTH_TOKEN=$(echo "$ACCESS_TOKEN" | cut -d ' ' -f 2 )
        echo "got token" ${GCS_OAUTH_TOKEN:0:5}
     fi
 
+    set -o errexit
+    set -o nounset
+    set -o pipefail
+
+
     /opt/samtools/bin/samtools mpileup --no-baq ~{if defined(roi_bed) then "-l ~{roi_bed}" else ""} -f "~{reference}" "~{normal_bam}" "~{tumor_bam}" | \
     java -jar /opt/varscan/VarScan.jar somatic /dev/stdin \
     "output" \