Replace NaN with 0 in forced integer columns of LIMS tables #583
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| name: cd | |
| on: | |
| pull_request: | |
| branches: [main] | |
| types: [closed] | |
| workflow_dispatch: | |
| jobs: | |
| build_push_metatlas_shifter_image: | |
| name: Build/push doejgi/metatlas_shifter docker image | |
| if: github.repository == 'biorack/metatlas' && (github.event.pull_request.merged || github.event_name == 'workflow_dispatch') | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: Login to GHCR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: generate version_info file | |
| run: python ./docker/most_recent_commits.py > docker/.version_info | |
| - name: generate time based tag | |
| id: timestamp | |
| run: | | |
| DATE_TIME=$(date -u +"%Y%m%d_%H%M%S") | |
| echo "date_time=${DATE_TIME}" >> $GITHUB_OUTPUT | |
| - name: Build Docker images # This is for the targeted metatlas pipeline | |
| id: build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./docker | |
| file: ./docker/Dockerfile.shifter | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=ghcr.io/biorack/metatlas/metatlas_shifter:latest | |
| cache-to: type=inline | |
| tags: | | |
| ghcr.io/biorack/metatlas/metatlas_shifter:${{ steps.timestamp.outputs.date_time }} | |
| ghcr.io/biorack/metatlas/metatlas_shifter:latest | |
| push: true | |
| build_push_metatlas_analysis_image: | |
| name: Build/push analysis docker image | |
| if: github.repository == 'biorack/metatlas' && (github.event.pull_request.merged || github.event_name == 'workflow_dispatch') | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: generate time based tag | |
| id: timestamp | |
| run: | | |
| DATE_TIME=$(date -u +"%Y%m%d_%H%M%S") | |
| echo "date_time=${DATE_TIME}" >> $GITHUB_OUTPUT | |
| - name: Login to GHCR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build Docker images # This is for the boutique analysis tasks | |
| id: build_analysis | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./docker | |
| file: ./docker/Dockerfile.analysis | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=ghcr.io/biorack/metatlas/analysis:latest | |
| cache-to: type=inline | |
| tags: | | |
| ghcr.io/biorack/metatlas/analysis:${{ steps.timestamp.outputs.date_time }} | |
| ghcr.io/biorack/metatlas/analysis:latest | |
| push: true | |
| build_push_metatlas_mzmine_image: | |
| name: Build/push mzmine docker image | |
| if: github.repository == 'biorack/metatlas' && (github.event.pull_request.merged || github.event_name == 'workflow_dispatch') | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: generate time based tag | |
| id: timestamp | |
| run: | | |
| DATE_TIME=$(date -u +"%Y%m%d_%H%M%S") | |
| echo "date_time=${DATE_TIME}" >> $GITHUB_OUTPUT | |
| - name: Login to GHCR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build Docker images # This is for the mzmine container | |
| id: build_mzmine | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./docker | |
| file: ./docker/Dockerfile.mzmine | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=ghcr.io/biorack/metatlas/mzmine:latest | |
| cache-to: type=inline | |
| tags: | | |
| ghcr.io/biorack/metatlas/mzmine:${{ steps.timestamp.outputs.date_time }} | |
| ghcr.io/biorack/metatlas/mzmine:latest | |
| push: true |