Rewrite the SplitVariants task command in TasksGenotypeBatch.wdl to call svtk only once #655
Workflow file for this run
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| name: Docker Images | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - 'src/**' | |
| - 'dockerfiles/**' | |
| - 'scripts/docker/build_docker.py' | |
| - '.github/workflows/sv_pipeline_docker.yml' | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - 'src/**' | |
| - 'dockerfiles/**' | |
| - 'scripts/docker/build_docker.py' | |
| - '.github/workflows/sv_pipeline_docker.yml' | |
| jobs: | |
| build_args_job: | |
| runs-on: ubuntu-20.04 | |
| name: Determine Build Args | |
| env: | |
| GITHUB_CONTEXT: ${{ toJson(github) }} | |
| outputs: | |
| base_sha: ${{ steps.commit_sha.outputs.BASE_SHA }} | |
| head_sha: ${{ steps.commit_sha.outputs.HEAD_SHA }} | |
| image_tag: ${{ steps.image_tag.outputs.IMAGE_TAG }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| # By default, this checks out only the current commit; | |
| # however, since a diff between the current commit and | |
| # the base commit is required to determined which docker | |
| # images to rebuild, we use the following to check out | |
| # the complete git history. | |
| fetch-depth: 0 | |
| - name: Determine Commit SHAs | |
| id: commit_sha | |
| # This action determines the SHA of two commits: | |
| # - BASE (BASE_SHA): The commit SHA of the base branch (e.g., | |
| # broadinstitute/gatk-sv:main) which the feature branch targets. | |
| # - HEAD (HEAD_SHA): The commit SHA of the latest commit on the | |
| # feature branch. | |
| # | |
| # In the following example, BASE_SHA=B and HEAD_SHA=Z | |
| # | |
| # X---Y---Z feature | |
| # / \ | |
| # A---B---C---D---E main | |
| # | |
| # 'E' is the merge commit (e.g., 'Merge pull request #0'). | |
| # | |
| # This action can be invoked as a result of (a) pushing commits X, | |
| # Y, or Z, or (b) pushing merge commit E (i.e., merging the PR). | |
| # Depending on (a) and (b) the commit SHAs are determined differently. | |
| # In case of (a), the commit SHAs are extracted from the | |
| # 'event.pull_request' key in the github's context JSON. In case of | |
| # (b), the commit SHAs are extracted from the list of commits recorded | |
| # under the 'event' key. | |
| # | |
| # Note: Github's context JSON is printed in the action's debug page. | |
| # | |
| run: | | |
| echo "::debug::EVENT_NAME: ${{ github.event_name }}" | |
| if [[ ${{ github.event_name }} == "pull_request" ]]; then | |
| BASE_SHA=${{ github.event.pull_request.base.sha }} | |
| HEAD_SHA=${{ github.event.pull_request.head.sha }} | |
| else | |
| BASE_SHA=${{ github.event.before }} | |
| HEAD_SHA=$(echo "$GITHUB_CONTEXT" | jq '.event.commits[].id' | tail -2 | head -1 | sed 's/\"//g') | |
| fi | |
| echo "::debug::BASE_SHA: $BASE_SHA" | |
| echo "::debug::HEAD_SHA: $HEAD_SHA" | |
| # Avail the determined commit SHAs to other steps. | |
| echo "BASE_SHA=$BASE_SHA" >> $GITHUB_OUTPUT | |
| echo "HEAD_SHA=$HEAD_SHA" >> $GITHUB_OUTPUT | |
| - name: Compose Image Tag | |
| id: image_tag | |
| # This step composes a tag to be used for all the images created by | |
| # the build_docker.py script. The tag follows the following template: | |
| # | |
| # DATE-RELEAST_TAG-HEAD_SHA_8 | |
| # | |
| # where 'DATE' is YYYY-MM-DD extracted from the time stamp of the last | |
| # commit on the feature branch (HEAD), `RELEASE_TAG` is extracted from | |
| # the latest [pre-]release on Github, and the 'HEAD_SHA_8' is the first | |
| # eight letters of the SHA of the last commit on the feature branch (HEAD). | |
| run: | | |
| # Extract the time stamp of COMMIT_SHA in YYYY-MM-DD format. | |
| # See git-show documentation available at: | |
| # http://schacon.github.io/git/git-show | |
| DATE=$(git show -s --format=%ad --date=format:'%Y-%m-%d' $COMMIT_SHA) | |
| # Get latest [pre-]release tag. | |
| RELEASE_TAG=$(jq -r '.[0] | .tag_name' <<< $(curl --silent https://api.github.com/repos/broadinstitute/gatk-sv/releases)) | |
| COMMIT_SHA=${{ steps.commit_sha.outputs.HEAD_SHA }} | |
| IMAGE_TAG=$DATE-$RELEASE_TAG-${COMMIT_SHA::8} | |
| echo "::debug::Image tag: $IMAGE_TAG" | |
| echo "IMAGE_TAG=$IMAGE_TAG" >> $GITHUB_OUTPUT | |
| build_job: | |
| runs-on: ubuntu-20.04 | |
| name: Test Images Build | |
| if: github.event_name == 'pull_request' | |
| needs: build_args_job | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| # See the comment on build_args_job. | |
| fetch-depth: 0 | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Run build_docker.py | |
| run: | | |
| cd ./scripts/docker/ | |
| python build_docker.py \ | |
| --base-git-commit ${{ needs.build_args_job.outputs.base_sha }} \ | |
| --current-git-commit ${{ needs.build_args_job.outputs.head_sha }} \ | |
| --image-tag ${{ needs.build_args_job.outputs.image_tag }} \ | |
| --prune-after-each-image | |
| publish_job: | |
| # This job first configures gcloud with the authentication of a | |
| # service account. It then uses gcloud to configure the docker | |
| # credentials. Finally, it rebuilds the docker images (targets are | |
| # determined by the `build_args_job`) and pushes them to GCR. | |
| name: Publish | |
| runs-on: ubuntu-20.04 | |
| environment: Deploy | |
| if: github.event_name == 'push' | |
| needs: build_args_job | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| env: | |
| DOCKERS_AZURE: "./inputs/values/dockers_azure.json" | |
| DOCKERS_GCP: "./inputs/values/dockers.json" | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| # See the comment on build_args_job. | |
| fetch-depth: 0 | |
| # Authenticates git using the bot's access token. | |
| token: ${{ secrets.BOT_PAT }} | |
| - name: Setup Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Azure login | |
| uses: azure/docker-login@v1 | |
| with: | |
| login-server: ${{ secrets.AZ_CR }} | |
| username: ${{ secrets.AZ_USERNAME }} | |
| password: ${{ secrets.AZ_PASSWORD }} | |
| - name: Setup gcloud CLI | |
| uses: google-github-actions/[email protected] | |
| with: | |
| project_id: ${{ secrets.GCP_PROJECT_ID }} | |
| service_account_key: ${{ secrets.GCP_GCR_SA_KEY }} | |
| # xref: https://github.com/google-github-actions/setup-gcloud#inputs | |
| # If you need to set `export_default_credentials: true` | |
| # make sure to pass the `--disable-git-protect` flag to | |
| # build_docker.py; because the setting export_default_credentials | |
| # to true will cause creating an untracked file in the root of | |
| # GATK-SV cloned directory which will cause build_docker.py to | |
| # raise an exception about the uncommitted file. | |
| - name: Configure Docker using gcloud | |
| # This step uses gcloud to configure docker credentials to access GCR | |
| # using a service account. | |
| # See: https://cloud.google.com/container-registry/docs/advanced-authentication | |
| # | |
| # The build_docker.py uses the `--squash` flag when building the | |
| # images to be pushed to GCR. This flag is only available when | |
| # experimental features are enabled, hence the features are enabled | |
| # in this flag. | |
| run: | | |
| gcloud auth configure-docker | |
| tmp=$(mktemp) | |
| sudo jq '.+{experimental:true}' /etc/docker/daemon.json > "$tmp" | |
| sudo mv "$tmp" /etc/docker/daemon.json | |
| sudo systemctl restart docker.service | |
| - name: Build and Publish Docker Images to ACR & GCR | |
| id: build_and_publish | |
| run: | | |
| 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 ${{ secrets.AZ_CR }} us.gcr.io/${{ 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 $DOCKERS_GCP \ | |
| --disable-git-protect \ | |
| --prune-after-each-image | |
| CHANGED=$(git diff --quiet $DOCKERS_GCP || echo True) | |
| echo "CHANGED=$CHANGED" >> $GITHUB_OUTPUT | |
| - name: Commit Changes to dockers_*.json | |
| if: steps.build_and_publish.outputs.CHANGED | |
| run: | | |
| COMMIT_SHA=${{ needs.build_args_job.outputs.head_sha }} | |
| git config --global user.name 'gatk-sv-bot' | |
| git config --global user.email '[email protected]' | |
| git commit $DOCKERS_AZURE $DOCKERS_GCP -m "Update docker images list, triggered by "${COMMIT_SHA::8} | |
| git pull --rebase origin main | |
| # In the following, force-push is required when the above rebase updates the branch; | |
| # otherwise, the push will be rejected with the following error: | |
| # > Updates were rejected because the tip of your current branch is behind ts remote counterpart. | |
| # See this thread for details: https://stackoverflow.com/q/39399804 | |
| git push -f |