Fix warnings in Github Actions (#8241)

* Updating action dependencies to newer versions that use the up to date version of node.js * Fixing deprecated set-output usage see https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/ * Fix typo fetch -> fetch-depth
broadinstitute · Mar 23, 2023 · 148dd33 · 148dd33
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commit 148dd33
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Showing 3 changed files with 27 additions and 26 deletions.
diff --git a/.github/actions/upload-gatk-test-results/action.yml b/.github/actions/upload-gatk-test-results/action.yml
@@ -34,7 +34,7 @@ runs:
   steps:
     - name: Upload test results
       if: always()
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       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 }}-${{ matrix.testType }}
@@ -51,7 +51,8 @@ runs:
         gsutil -m cp -z html -z js -z xml -z css -r build/reports/tests gs:/${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/;
         VIEW_URL=https://storage.googleapis.com${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/tests/testOnPackagedReleaseJar/index.html
         echo "See the test report at ${VIEW_URL}";
-        echo ::set-output name=view_url::"${VIEW_URL}"
+        echo view_url="${VIEW_URL}" >> $GITHUB_OUTPUT
+
       shell: bash
 
 # This code is necessary in order to extract the URL for the logs for a particular run. The github context exposes the run_id object
@@ -69,8 +70,8 @@ runs:
         eval "$(curl --get -Ss -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.v3+json" "${GITHUB_BASEURL}${GITHUB_API}?per_page=30" \
         | jq -r --arg job_name "${{ inputs.identifier }}" '.jobs | map(select(.name == $job_name)) | .[0] | @sh "job_id=\(.id) html_url=\(.html_url)"')"
 
-        echo ::set-output name=job_id::"${job_id}"
-        echo ::set-output name=html_url::"${html_url}"
+        echo job_id="${job_id}" >> $GITHUB_OUTPUT
+        echo html_url="${html_url}" >> $GITHUB_OUTPUT
         echo ${job_id}
         echo ${html_url}
       shell: bash

diff --git a/.github/workflows/gatk-nightly-docker.yml b/.github/workflows/gatk-nightly-docker.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout gatk
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml
@@ -32,37 +32,37 @@ jobs:
         env:
           GCP_CREDENTIALS: ${{ secrets.GCP_CREDENTIALS }}
         if: "${{ env.GCP_CREDENTIALS != '' }}"
-        run: echo "::set-output name=defined::true"
+        run: echo defined=true >> $GITHUB_OUTPUT
 
 
   buildDocker:
     name: build and push gatk docker to artifacts
     runs-on: ubuntu-latest
     steps:
       - name: checkout gatk
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v4
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
             type=raw,value=${{github.sha}}
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v4
         with:
           context: .
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           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@v2
+      - name: Upload docker image as artifact 
+        uses: actions/upload-artifact@v3
         with:
           name: gatkDockerImage
           path: /tmp/myimage.tar
@@ -84,11 +84,11 @@ jobs:
       SCALA_VERSION: ${{ matrix.scalaVersion }}
     name: Java ${{ matrix.Java }} build and test ${{ matrix.testType }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: 'Set up java ${{ matrix.Java }}'
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: ${{ matrix.Java }}
           distribution: 'temurin'
@@ -157,12 +157,12 @@ jobs:
 
     name: Java ${{ matrix.Java }} test on docker ${{matrix.testType}}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 #TODO make this shallow
 
       - name: 'Set up java ${{ matrix.Java }}'
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: ${{ matrix.Java }}
           distribution: 'temurin'
@@ -199,7 +199,7 @@ jobs:
           cp scripts/docker/dockertest.gradle .
 
       - name: Download docker image artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: gatkDockerImage
           path: /tmp
@@ -247,11 +247,11 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate script WDLs using womtools
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
-          fetch: 0
+          fetch-depth: 0
       - name: Set up java 17
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -267,11 +267,11 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate generated WDLs using womtools
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
-          fetch: 0
+          fetch-depth: 0
       - name: Set up java 17
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -292,13 +292,13 @@ jobs:
     continue-on-error: true
     name: WDL test ${{ matrix.wdlTest }} on cromwell
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: pull lfs files
         run: git lfs pull
       - name: Set up java 17
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -351,4 +351,4 @@ jobs:
         if: ${{ matrix.wdlTest == 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' }}
         run: |
           echo "Running VCF Site Level Filtering WDL";
-          bash scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh;
+          bash scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh;