VAT creation on GCP Batch [VS-1602]

.dockstore.yml

@@ -242,7 +242,6 @@ workflows:
          branches:
              - master
              - ah_var_store
-             - vs_1605_chr5_oops
          tags:
              - /.*/
    - name: GvsWithdrawSamples
@@ -316,8 +315,6 @@ workflows:
          branches:
              - master
              - ah_var_store
-             - vs_1418_ploidy_for_foxtrot_vds
-             - gg_VS-1584_build_variants_docker_on_m4
          tags:
              - /.*/
    - name: GvsIngestTieout

scripts/variantstore/variant-annotations-table/GvsCreateVATfromVDS.wdl

@@ -630,10 +630,17 @@ task AnnotateVCF {
 
             # Find where the reference disk should have been mounted on this VM.  Note this is referred to as a "candidate
             # mount point" because we do not actually confirm this is a reference disk until the following code block.
-            CANDIDATE_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
-            if [[ -z ${CANDIDATE_MOUNT_POINT} ]]; then
-                >&2 echo "Could not find a mounted volume that looks like a reference disk, exiting."
-                exit 1
+            if [[ -e /cromwell_root/gcs_delocalization.sh ]]
+            then
+              # PAPI mount points
+              CANDIDATE_MOUNT_POINT=$(lsblk | grep -v cromwell_root | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
+            elif [[ -e /mnt/disks/cromwell_root/gcs_delocalization.sh ]]
+            then
+              # GCP Batch mount points
+              CANDIDATE_MOUNT_POINT=$(lsblk | grep -v cromwell_root | sed -E -n 's!.*(/mnt/disks/[a-f0-9]+).*!\1!p')
+            else
+              >&2 echo "Could not find a mounted volume that looks like a reference disk, exiting."
+              exit 1
             fi
 
             # Find one particular reference under the mount path. Note this is not the same reference as was specified in the