v4 all the GitHub action things [VS-1573]

.github/actions/upload-gatk-test-results/action.yml

@@ -34,7 +34,7 @@ runs:
   steps:
     - name: Upload test results
       if: always()
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         # ternary expression syntax is workaround found here https://github.com/actions/runner/issues/409
         name: test-results-${{ inputs.is-docker == 'true' && 'docker-' ||  '' }}${{ matrix.Java }}-${{ matrix.testType }}

.github/workflows/gatk-nightly-docker.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout gatk
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/gatk-tests.yml

@@ -40,7 +40,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout gatk
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - uses: ./.github/actions/purge-runner-disk
 
@@ -64,7 +64,7 @@ jobs:
           outputs: type=docker,dest=/tmp/myimage.tar
       # By uploading the docker image as an artifact we save ourselves the requirement for the image to be built with ghcr push permission
       - name: Upload docker image as artifact 
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: gatkDockerImage
           path: /tmp/myimage.tar
@@ -86,12 +86,12 @@ jobs:
       SCALA_VERSION: ${{ matrix.scalaVersion }}
     name: Java ${{ matrix.Java }} build and test ${{ matrix.testType }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: ./.github/actions/purge-runner-disk
       - name: 'Set up java ${{ matrix.Java }}'
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.Java }}
           distribution: 'temurin'
@@ -160,14 +160,14 @@ jobs:
 
     name: Java ${{ matrix.Java }} test on docker ${{matrix.testType}}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 #TODO make this shallow
 
       - uses: ./.github/actions/purge-runner-disk
 
       - name: 'Set up java ${{ matrix.Java }}'
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.Java }}
           distribution: 'temurin'
@@ -204,7 +204,7 @@ jobs:
           cp scripts/docker/dockertest.gradle .
 
       - name: Download docker image artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: gatkDockerImage
           path: /tmp
@@ -252,12 +252,12 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate script WDLs using womtools
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: ./.github/actions/purge-runner-disk
       - name: Set up java 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -273,12 +273,12 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate generated WDLs using womtools
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: ./.github/actions/purge-runner-disk
       - name: Set up java 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -299,14 +299,14 @@ jobs:
     continue-on-error: true
     name: WDL test ${{ matrix.wdlTest }} on cromwell
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: ./.github/actions/purge-runner-disk
       - name: pull lfs files
         run: git lfs pull
       - name: Set up java 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'temurin'