updated note about apptainer cache dir #94
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| name: Run pipeline tests and deploy to registry | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| tags: | |
| - '[0-9]+.[0-9]+' | |
| - '[0-9]+.[0-9]+.[0-9]+' | |
| - '.+-rc[0-9]' | |
| pull_request: | |
| branches: | |
| - 'master' | |
| schedule: | |
| - cron: '0 6 15 * *' # 15th of each month at 6am | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| test_and_publish: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log into registry ${{ env.REGISTRY }} | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract Docker metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: Build Docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| context: "{{defaultContext}}:docker" | |
| labels: ${{ steps.meta.outputs.labels }} | |
| load: true | |
| push: false | |
| tags: | | |
| ${{ steps.meta.outputs.tags }} | |
| gha_image | |
| - name: Install Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: latest | |
| - run: nextflow -quiet run main.nf -params-file test/minimal/params.json -profile docker --container gha_image | |
| - run: nextflow -quiet run main.nf -params-file test/its/params.json -profile docker --container gha_image | |
| - run: nextflow -quiet run main.nf -params-file test/noindex/params.json -profile docker --container gha_image | |
| - run: nextflow -quiet run main.nf -params-file test/single/cmsearch/params.json -profile docker --container gha_image | |
| - run: nextflow -quiet run main.nf -params-file test/single/vsearch/params.json -profile docker --container gha_image | |
| - run: nextflow -quiet run main.nf -params-file test/minimal/params.json -profile docker --container gha_image --manifest test/minimal/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/its/params.json -profile docker --container gha_image --manifest test/its/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/noindex/params.json -profile docker --container gha_image --manifest test/noindex/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/single/cmsearch/params.json -profile docker --container gha_image --manifest test/single/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/single/vsearch/params.json -profile docker --container gha_image --manifest test/single/manifest.csv | |
| - run: docker run --volume $(pwd):$(pwd) --workdir $(pwd) gha_image /bin/bash -c "cd test/ungs/;./test_combine_svs.sh" | |
| - name: Push tag to ${{ env.REGISTRY }} | |
| if: github.ref_type == 'tag' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| annotations: ${{ steps.meta.outputs.annotations }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| context: "{{defaultContext}}:docker" | |
| labels: ${{ steps.meta.outputs.labels }} | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} |