Nextflow initital implementation for containerization #1
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| name: Build and Push Docker Container | |
| on: | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - 'v*' | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| env: | |
| REGISTRY: docker.io | |
| IMAGE_NAME: triton | |
| jobs: | |
| build-and-push: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log in to Docker Hub | |
| if: github.event_name != 'pull_request' | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Extract metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ secrets.DOCKERHUB_USERNAME }}/${{ env.IMAGE_NAME }} | |
| tags: | | |
| type=ref,event=branch | |
| type=ref,event=pr | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=raw,value=latest,enable={{is_default_branch}} | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| - name: Generate Singularity recipe | |
| if: github.event_name != 'pull_request' | |
| run: | | |
| echo "Bootstrap: docker" > Singularity.def | |
| echo "From: ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.IMAGE_NAME }}:latest" >> Singularity.def | |
| echo "" >> Singularity.def | |
| echo "%help" >> Singularity.def | |
| echo " Triton - cfDNA fragmentomics and nucleosome analysis pipeline" >> Singularity.def | |
| echo " See https://github.com/${{ github.repository }} for more information" >> Singularity.def | |
| - name: Upload Singularity recipe | |
| if: github.event_name != 'pull_request' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: singularity-recipe | |
| path: Singularity.def |