feat: deduplicate with UMIs #251
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Docker develop containers | |
| on: | |
| push: | |
| branches: | |
| - "develop" | |
| pull_request: | |
| branches-ignore: | |
| - "master" | |
| paths: | |
| - "BALSAMIC/containers/**" | |
| jobs: | |
| main: | |
| name: Build and publish | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, multiqc, msisensorpro, purecn, somalier, varcall_py3, varcall_py27, vcf2cytosure] | |
| steps: | |
| - name: Git checkout | |
| id: git_checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Login to Docker Hub | |
| id: docker_login | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Build and push | |
| id: docker_build_push | |
| uses: docker/build-push-action@v3 | |
| with: | |
| file: BALSAMIC/containers/${{ matrix.container-name }}/Dockerfile | |
| push: true | |
| tags: clinicalgenomics/balsamic:develop-${{ matrix.container-name }} | |
| build-args: CONTAINER_NAME=${{ matrix.container-name }} | |
| provenance: false | |
| - name: Prune containers | |
| id: docker_prune_containers | |
| shell: bash | |
| run: | | |
| docker system prune -a -f | |
| - name: Test container | |
| id: docker_test_container | |
| shell: bash | |
| run: | | |
| docker run \ | |
| -v $(readlink -f container_tests):/container_tests \ | |
| clinicalgenomics/balsamic:develop-${{ matrix.container-name }} \ | |
| bash /container_tests/${{ matrix.container-name }}/${{ matrix.container-name }}.sh |