Add 'gtex' profile to pipeline tests #50
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| name: Test | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| branches: | |
| - master | |
| env: | |
| JAVA_VERSION: 17 | |
| JAVA_DISTRO: zulu | |
| AWS_REGION: us-east-1 | |
| permissions: | |
| id-token: write | |
| contents: read | |
| jobs: | |
| pipeline-test: | |
| name: Pipeline tests | |
| runs-on: ubuntu-latest | |
| needs: [module-test, workflow-test] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| profile: | |
| - gemflux | |
| - starrsem | |
| - starflux | |
| - markdup | |
| - rmdup | |
| - ihec | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::566365074765:role/github-actions-role | |
| aws-region: ${{ env.AWS_REGION }} | |
| - name: Login to Amazon ECR Public | |
| id: login-ecr-public | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| with: | |
| registry-type: public | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: ${{ env.JAVA_DISTRO }} | |
| java-version: ${{ env.JAVA_VERSION }} | |
| java-package: jre | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - name: Run tests | |
| run: nf-test test --tag pipeline --profile +${CI_PROFILE} | |
| env: | |
| CI_PROFILE: ${{ matrix.profile }} | |
| workflow-test: | |
| name: Workflow tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::566365074765:role/github-actions-role | |
| aws-region: ${{ env.AWS_REGION }} | |
| - name: Login to Amazon ECR Public | |
| id: login-ecr-public | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| with: | |
| registry-type: public | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: ${{ env.JAVA_DISTRO }} | |
| java-version: ${{ env.JAVA_VERSION }} | |
| java-package: jre | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - name: Run tests | |
| run: nf-test test --tag workflow | |
| module-test: | |
| name: Module tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::566365074765:role/github-actions-role | |
| aws-region: ${{ env.AWS_REGION }} | |
| - name: Login to Amazon ECR Public | |
| id: login-ecr-public | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| with: | |
| registry-type: public | |
| - name: Set up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: ${{ env.JAVA_DISTRO }} | |
| java-version: ${{ env.JAVA_VERSION }} | |
| java-package: jre | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - name: Run tests | |
| run: nf-test test --tag module |