tweak

scripts/variantstore/wdl/GvsCreateVATfromVDS.wdl

@@ -320,12 +320,8 @@ task AnnotateVCF {
         String output_annotated_file_name
         File custom_annotations_file
 
-        # These "inputs" do not need to be provided by the caller, these are listed here so Cromwell will connect the
-        # Nirvana reference image and create the appropriate symlinks.
-        # Specific Nirvana references sourced from firecloud-develop cromwell-reference-images.conf.
-
         # Mentioning this path in the inputs section of the task combined with checking the 'Use reference disks' option
-        # in Terra UI should cause Cromwell to arrange for the Nirvana reference disk to be attached to this VM.
+        # in Terra UI tells Cromwell to arrange for the Nirvana reference disk to be attached to this VM.
         File summon_reference_disk =
             "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/References/Homo_sapiens.GRCh38.Nirvana.dat"
     }
@@ -350,15 +346,18 @@ task AnnotateVCF {
         set -o errexit -o nounset -o pipefail -o xtrace
 
         # There's an issue with how the projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-01-03
-        # disk image was built and while all the reference files do exist on the image they are not at the expected
-        # locations. The following two lines of code work around this problem until a corrected image is built with the
-        # references at the expected locations.
+        # disk image was built: while all the reference files do exist on the image they are not at the expected
+        # locations. The following code works around this issue and should continue to work even after a corrected
+        # version of the Nirvana reference image is deployed into Terra.
 
         # Find where the reference disk has been mounted on this VM:
         REFERENCE_DISK_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
 
-        # Point to where the references actually exist on this image:
-        DATA_SOURCES_FOLDER="${REFERENCE_DISK_MOUNT_POINT}/nirvana-references/nirvana-3-18-1"
+        # Find this one particular reference under the mount path:
+        GRCH38_PATH=$(find ${REFERENCE_DISK_MOUNT_POINT} -name Homo_sapiens.GRCh38.Nirvana.dat)
+
+        # Take the parent of the parent directory of this file as root of the locally mounted references:
+        DATA_SOURCES_FOLDER="$(dirname $(dirname ${GRCH38_PATH}))"
 
         # =======================================
         echo "Creating custom annotations"