Update gatk-reference.wdl #760
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| name: Workflows Docker Build | |
| on: | |
| push: | |
| env: | |
| REGISTRY: ghcr.io | |
| jobs: | |
| list-images: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| images: ${{ steps.set-matrix.outputs.images }} | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set matrix | |
| id: set-matrix | |
| run: echo "images=$(find docker -maxdepth 2 -mindepth 2 -not -path "*/cellranger/*" | jq --raw-input --slurp --compact-output 'split("\n")[:-1]')" >> $GITHUB_OUTPUT | |
| build-images: | |
| needs: list-images | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| image: ${{ fromJson(needs.list-images.outputs.images) }} | |
| steps: | |
| - name: Set Env | |
| run: | | |
| echo "TOOL=$(basename `dirname "${{ matrix.image }}"` | awk '{print tolower($0)}')" >> $GITHUB_ENV | |
| echo "SEMVER=$(basename "${{ matrix.image }}")" >> $GITHUB_ENV | |
| echo "IMAGE_TAG=$(basename "${{ matrix.image }}")" >> $GITHUB_ENV | |
| echo "GH_REF=${GITHUB_REF##*/}" >> $GITHUB_ENV | |
| - name: Set Branch Tag | |
| if: github.ref != 'refs/heads/main' | |
| run: echo "IMAGE_TAG=branch-${GITHUB_REF##*/}-${{ env.SEMVER }}" >> $GITHUB_ENV | |
| - uses: actions/checkout@v3 | |
| - name: Log in to the Container registry | |
| run: echo ${{ secrets.GITHUB_TOKEN }} | docker login ${{ env.REGISTRY }} --username ${{ github.actor }} --password-stdin | |
| - uses: webfactory/ssh-agent@v0.7.0 | |
| with: | |
| ssh-private-key: ${{ secrets.STJUDE_SEQERR_READONLY_DEPLOY_KEY }} | |
| - uses: docker/setup-qemu-action@v2 | |
| - uses: docker/setup-buildx-action@v2 | |
| - uses: docker/build-push-action@v4 | |
| with: | |
| context: ${{ matrix.image }} | |
| push: true | |
| ssh: default | |
| tags: ${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ env.TOOL }}:${{ env.IMAGE_TAG }} | |
| cache-from: type=registry,ref=${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ env.TOOL }}:buildcache | |
| cache-to: type=registry,ref=${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ env.TOOL }}:buildcache,mode=max |