fix: umi coverage qc (#1490) #344
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| 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 |