Fix a bug committing changes to dockers_*.json after an image is upda…

…ted (#559) * Fig bug setting env. var & pass azure docker repo. * Update the dockers list.
broadinstitute · Jun 27, 2023 · 4f29bd5 · 4f29bd5
1 parent 0be9cf8
commit 4f29bd5
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/.github/workflows/sv_pipeline_docker.yml b/.github/workflows/sv_pipeline_docker.yml
@@ -209,14 +209,14 @@ jobs:
           python ./scripts/docker/build_docker.py \
             --base-git-commit ${{ needs.build_args_job.outputs.base_sha }} \
             --current-git-commit ${{ needs.build_args_job.outputs.head_sha }} \
-            --docker-repo us.gcr.io/${{ secrets.GCP_PROJECT_ID }}/gatk-sv \
+            --docker-repo ${{ secrets.AZ_CR }} us.gcr.io/${{ secrets.GCP_PROJECT_ID }}/gatk-sv \
             --image-tag ${{ needs.build_args_job.outputs.image_tag }} \
             --input-json $DOCKERS_AZURE $DOCKERS_GCP \
             --output-json $DOCKERS_AZURE $DOCKERS_GCP \
             --disable-git-protect
           
           CHANGED=$(git diff --quiet $DOCKERS_GCP || echo True)
-          echo "::set-output name=CHANGED::$CHANGED"
+          echo "CHANGED=$CHANGED" >> $GITHUB_OUTPUT
 
       - name: Commit Changes to dockers_*.json
         if: steps.build_and_publish.outputs.CHANGED

diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -13,7 +13,7 @@
   "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2023-02-01-v0.26.8-beta-9b25c72d",
   "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/vjalili/sv-base-mini:5994670",
   "sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
-  "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
+  "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-06-27-v0.27.3-beta-0be9cf8a",
   "sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
   "sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
   "sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",

diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json
@@ -13,7 +13,7 @@
   "sv_base_docker": "vahid.azurecr.io/gatk-sv/sv-base:2023-02-01-v0.26.8-beta-9b25c72d",
   "sv_base_mini_docker": "vahid.azurecr.io/vjalili/sv-base-mini:5994670",
   "sv_pipeline_base_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
-  "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
+  "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2023-06-27-v0.27.3-beta-0be9cf8a",
   "sv_pipeline_hail_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
   "sv_pipeline_updates_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",
   "sv_pipeline_qc_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2023-05-24-v0.27.3-beta-1796b665",