Merge pull request #592 from umccr/dragen-instrument-run-fastq-to-ora… #220
Workflow file for this run
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| name: Create Workflow Release Asset | |
| on: | |
| push: | |
| tags: | |
| # Matches dragen-pon-qc/3.9.3 | |
| # Matches tso500-ctdna-with-post-processing-pipeline/1.1.0--1.0.0 | |
| # Matches dragen-somatic-pipeline/4.0.3-rc | |
| # ** required since our tags have '/' in them -- https://stackoverflow.com/a/61892639/6946787 | |
| # Single quotes required since * is a special character in yaml | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet | |
| - '**' | |
| jobs: | |
| # Workflow split due to https://github.com/actions/runner/issues/662 | |
| # This way we do a 'precheck', update a few vars and most importantly make sure that the tag is legix | |
| release_asset_precheck: | |
| name: release asset precheck | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| # Checkout code | |
| - name: Checkout code | |
| id: git_checkout | |
| uses: actions/checkout@v4 | |
| # Set to fail | |
| - name: Update bash settings | |
| id: update_bash_settings | |
| run: | | |
| set -euo pipefail | |
| # Install jq (for querying branch name) | |
| - name: Install Jq | |
| id: install_jq | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install jq -y | |
| # Get tag | |
| - name: Set output | |
| id: get_tag | |
| run: echo "tag=${GITHUB_REF#refs/*/}" >> $GITHUB_OUTPUT | |
| # Ensure tag matches regex | |
| - name: action regex match | |
| id: tag_regex_match | |
| uses: kaisugi/[email protected] | |
| with: | |
| text: ${{ steps.get_tag.outputs.tag }} | |
| regex: '^[A-Za-z0-9-_]+/[0-9]+\.[0-9]+\.[0-9]+(?:--\S+)?(-rc)?$' | |
| # Get email and username | |
| - name: Get User Configurations | |
| id: get_user_configurations | |
| run: | | |
| echo "user_name=${{ github.actor }}" >> "${GITHUB_OUTPUT}" | |
| echo "user_email=${{ github.actor_id }}+${{ github.actor }}@users.noreply.github.com" >> "${GITHUB_OUTPUT}" | |
| # Has regex match | |
| - name: has regex match | |
| id: has_regex_match | |
| run: | | |
| create_release="false" | |
| is_prerelease="false" | |
| if [[ -n "${{ steps.tag_regex_match.outputs.match }}" ]]; then | |
| create_release="true" | |
| fi | |
| if [[ -n "${{ steps.tag_regex_match.outputs.group1 }}" ]]; then | |
| is_prerelease="true" | |
| fi | |
| echo "create_release=${create_release}" >> "${GITHUB_OUTPUT}" | |
| echo "is_prerelease=${is_prerelease}" >> "${GITHUB_OUTPUT}" | |
| # Get date | |
| - name: get date | |
| id: get_date | |
| run: | | |
| echo "date_str=$(date +%Y%m%d%H%M%S)" >> "${GITHUB_OUTPUT}" | |
| # Get workflow path | |
| - name: get workflow path | |
| id: get_workflow_path | |
| run: | | |
| # Get tag without release candidate | |
| tag="${{ steps.get_tag.outputs.tag }}" | |
| tag="${tag//-rc}" | |
| # Check workflow directory exists | |
| if [[ ! -d "workflows/$tag" ]]; then | |
| echo "Could not find directory workflows/$tag" | |
| exit 1 | |
| fi | |
| workflow_path="$( \ | |
| find "workflows/$tag" \ | |
| -mindepth 1 \ | |
| -maxdepth 1 \ | |
| -type f \ | |
| -name "*.cwl" | |
| )" | |
| echo "workflow_path=${workflow_path}" >> "${GITHUB_OUTPUT}" | |
| # Set git tag env var | |
| - name: set git tag | |
| id: set_git_tag | |
| run: | | |
| echo "git_tag=${{ steps.get_tag.outputs.tag }},${{ steps.get_tag.outputs.tag }}__${{ steps.get_date.outputs.date_str }}" >> "${GITHUB_OUTPUT}" | |
| # Set up complete | |
| # Set outputs | |
| outputs: | |
| original_tag: ${{ steps.get_tag.outputs.tag }} | |
| git_tag: ${{ steps.set_git_tag.outputs.git_tag }} | |
| user_name: ${{ steps.get_user_configurations.outputs.user_name }} | |
| user_email: ${{ steps.get_user_configurations.outputs.user_email }} | |
| workflow_path: ${{ steps.get_workflow_path.outputs.workflow_path }} | |
| create_release: ${{ steps.has_regex_match.outputs.create_release }} | |
| is_prerelease: ${{ steps.has_regex_match.outputs.is_prerelease }} | |
| get_umccr_prod_icav2_access_token: | |
| # Note this currently gets the access token for the 'trial' project | |
| name: Get ICAv2 Access Token (umccr-prod) | |
| uses: ./.github/workflows/get_tenant_icav2_access_token.yml | |
| with: | |
| role_to_assume_arn: arn:aws:iam::472057503814:role/gh-service-icav2-pipeline-user-prod | |
| secret_arn: arn:aws:secretsmanager:ap-southeast-2:472057503814:secret:ICAv2JWTKey-umccr-prod-service-pipelines-WoiHJv | |
| secrets: | |
| symmetrical_encryption_key: ${{ secrets.SYMMETRICAL_ENCRYPTION_KEY }} | |
| create_release_asset: | |
| name: create release asset | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| needs: | |
| - release_asset_precheck | |
| - get_umccr_prod_icav2_access_token | |
| steps: | |
| # Checkout code | |
| - name: Checkout code | |
| id: git_checkout | |
| uses: actions/checkout@v4 | |
| # Decrypt tokens | |
| - id: decrypt_umccr_prod_icav2_access_token | |
| name: Decrypt Access Token | |
| uses: ./.github/actions/decrypt_token | |
| with: | |
| encrypted_token: ${{ needs.get_umccr_prod_icav2_access_token.outputs.icav2_access_token_encrypted }} | |
| decryption_key: ${{ secrets.SYMMETRICAL_ENCRYPTION_KEY }} | |
| # Create release asset | |
| - name: create release asset | |
| id: create_release_asset | |
| if: needs.release_asset_precheck.outputs.create_release == 'true' | |
| run: | | |
| docker run \ | |
| --rm \ | |
| --volume "$PWD:$PWD" \ | |
| --workdir "$PWD" \ | |
| --env CWL_ICA_REPO_PATH="${PWD}" \ | |
| --env GITHUB_SERVER_URL="${GITHUB_SERVER_URL}" \ | |
| --env GITHUB_REPOSITORY="${GITHUB_REPOSITORY}" \ | |
| --env GITHUB_TAG="${{ needs.release_asset_precheck.outputs.git_tag }}" \ | |
| --env GITHUB_TOKEN="${{ secrets.GITHUB_TOKEN }}" \ | |
| --env _GIT_AUTHOR_NAME="${{ needs.release_asset_precheck.outputs.user_name }}" \ | |
| --env _GIT_AUTHOR_EMAIL="${{ needs.release_asset_precheck.outputs.user_email }}" \ | |
| --env ICAV2_ACCESS_TOKEN_UMCCR_PROD="${{ steps.decrypt_umccr_prod_icav2_access_token.outputs.decrypted_token }}" \ | |
| ghcr.io/umccr/cwl-ica-cli:latest \ | |
| bash ".github/scripts/create_workflow_release_asset.sh" \ | |
| --workflow-path "${{ needs.release_asset_precheck.outputs.workflow_path }}" \ | |
| --is-prerelease "${{ needs.release_asset_precheck.outputs.is_prerelease }}" |