update to use v1.2.2 of the wdl pipelines and v87 of cromwell

wustl-oncology · Nov 26, 2024 · 42d8bb8 · 42d8bb8
1 parent d47e34c
commit 42d8bb8
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/manual-workflows/start.sh b/manual-workflows/start.sh
@@ -18,7 +18,7 @@ arguments:
 --workflow-options   Local path to workflow_options.json. DEFAULT \$SRC_DIR/workflow_options.json
 --machine-type       GCP machine type for the instance. DEFAULT e2-standard-2
 --zone               DEFAULT us-central1-c. For options, visit: https://cloud.google.com/compute/docs/regions-zones 
---analysis-release   DEFAULT 1.1.4. For options, visit: https://github.com/wustl-oncology/analysis-wdls/releases
+--analysis-release   DEFAULT 1.2.2. For options, visit: https://github.com/wustl-oncology/analysis-wdls/releases
 
 Additional arguments are passed directly to gsutil compute instances
 create command. For more information on those arguments, check that commands
@@ -100,7 +100,7 @@ while test $# -gt 0; do
             ;;
         --analysis-release*)
             if [ ! "$2" ]; then
-                ANALYSIS_RELEASE="1.1.4"
+                ANALYSIS_RELEASE="1.2.2"
             else
                 ANALYSIS_RELEASE=$2
                 shift
@@ -120,7 +120,7 @@ MACHINE_TYPE=${MACHINE_TYPE:-"e2-standard-2"}
 [ -z $CROMWELL_CONF    ] && CROMWELL_CONF="$SRC_DIR/cromwell.conf"
 [ -z $WORKFLOW_OPTIONS ] && WORKFLOW_OPTIONS="$SRC_DIR/workflow_options.json"
 [ -z $ZONE             ] && ZONE="us-central1-c"
-[ -z $ANALYSIS_RELEASE ] && ANALYSIS_RELEASE="1.1.4"
+[ -z $ANALYSIS_RELEASE ] && ANALYSIS_RELEASE="1.2.2"
 
 if [[ ! -f $CROMWELL_CONF ]]; then
     cat <<EOF
@@ -152,7 +152,7 @@ gcloud compute instances create $INSTANCE_NAME \
        --machine-type=$MACHINE_TYPE \
        --service-account=$SERVER_ACCOUNT --scopes=cloud-platform \
        --network=$NETWORK --subnet=$SUBNET \
-       --metadata=cromwell-version=71,analysis-release="$ANALYSIS_RELEASE" \
+       --metadata=cromwell-version=87,analysis-release="$ANALYSIS_RELEASE" \
        --metadata-from-file=startup-script=$SRC_DIR/server_startup.py,cromwell-conf=$CROMWELL_CONF,helpers-sh=$SRC_DIR/helpers.sh,cromwell-service=$SRC_DIR/cromwell.service,workflow-options=$WORKFLOW_OPTIONS,persist-artifacts=$SRC_DIR/../scripts/persist_artifacts.py \
        $@