Update update_pango_aliasor.yml

StaPH-B · Dec 9, 2024 · 1548ab2 · 1548ab2
1 parent 920cc16
commit 1548ab2
Showing 1 changed file with 25 additions and 18 deletions.
diff --git a/.github/workflows/update_pango_aliasor.yml b/.github/workflows/update_pango_aliasor.yml
@@ -1,33 +1,32 @@
 ##### ------------------------------------------------------------------------------------------------ #####
 ##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
-##### recent version of pango_aliasor and downloads the current pangolin lineages.                     #####
+##### recent version of Freyja and downloading the most recent variant information.                    #####
 ##### It takes no manual input.                                                                        #####
 ##### ------------------------------------------------------------------------------------------------ #####
 
-name: Update pango aliasor
+name: Update Freyja
 
 on: 
   workflow_dispatch:
   schedule:
     - cron: '30 7 * * 1'
 
-run-name: Updating pango aliasor
+run-name: Updating Freyja
 
 jobs:
   update:
     runs-on: ubuntu-latest
-    steps:
-
+    steps:    
       - name: pull repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4     
 
-      - name: set pango_aliasor version
+      - name: set freyja version
         id: latest_version
         run: |
-          version=0.3.0
+          version=1.5.2
           echo "version=$version" >> $GITHUB_OUTPUT 
           
-          file=pango_aliasor/0.3.0/Dockerfile
+          file=freyja/$version/Dockerfile
           ls $file
           echo "file=$file" >> $GITHUB_OUTPUT
 
@@ -39,11 +38,19 @@ jobs:
         id: docker_build_to_test
         uses: docker/build-push-action@v5
         with:
-          context: pango_aliasor/${{ steps.latest_version.outputs.version }}
+          file: ${{ steps.latest_version.outputs.file }}
           target: test
           load: true
           push: false
-          tags: pango_aliasor:update
+          tags: freyja:update
+
+      - name: get freyja database version
+        id: db_version
+        run: |
+          docker run freyja:update freyja demix --version
+          version=$(docker run freyja:update freyja demix --version | grep . | grep -v Barcode | head -n 1)
+          echo "the latest version is $version"
+          echo "version=$version" >> $GITHUB_OUTPUT
 
       - name: Get current date
         id: date
@@ -65,18 +72,18 @@ jobs:
           username: ${{ secrets.QUAY_USERNAME }}
           password: ${{ secrets.QUAY_ROBOT_TOKEN }}
 
-      - name: Build and push user-defined tag to DockerHub
-        id: docker_build_user_defined_tag
+      - name: Build and push Dockerfile
+        id: docker_build_and_push
         uses: docker/build-push-action@v5
         with:
           file: ${{ steps.latest_version.outputs.file }}
           target: app
           push: true
           tags: |
-            staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
-            staphb/pango_aliasor:latest
-            quay.io/staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
-            quay.io/staphb/pango_aliasor:latest
+            staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            staphb/freyja:latest
+            quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }}
+            quay.io/staphb/freyja:latest
 
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: echo ${{ steps.docker_build_user_defined_tag.outputs.digest }}