Improve readTsv function #54
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: 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 | |
| - gtex | |
| 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 |