Run Pipeline Tests #10
Workflow file for this run
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| name: Run Pipeline Tests | |
| on: | |
| workflow_dispatch | |
| env: | |
| NEXTFLOW_VERSION: 23.10.1 | |
| NF_TEST_VERSION: 0.8.3 | |
| jobs: | |
| clean_start: | |
| name: Clean workspace before start | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/[email protected] | |
| - run: rm -rf $GITHUB_WORKSPACE/* | |
| jdk_setup: | |
| name: Set up JDK 17 | |
| needs: clean_start | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| nextflow_install: | |
| name: Install nextflow | |
| needs: jdk_setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow | |
| nf_test_install: | |
| name: Install nf-test | |
| needs: nextflow_install | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: sudo bash; cd /opt; wget "https://github.com/askimed/nf-test/releases/download/v${NF_TEST_VERSION}/nf-test-${NF_TEST_VERSION}.tar.gz"; tar -xvf "nf-test-${NF_TEST_VERSION}.tar.gz"; chmod +x nf-test; rm "/opt/nf-test-${NF_TEST_VERSION}.tar.gz" | |
| append_path: | |
| name: Add software to path | |
| needs: nf_test_install | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: echo "/opt" >> $GITHUB_PATH | |
| test_download: | |
| name: Run ncbi_download test | |
| needs: append_path | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: nf-test test tests/modules/download_ncbi.nf.test | |
| test_gffread: | |
| name: Run gffread test | |
| needs: append_path | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: nf-test test tests/modules/gffread.nf.test | |
| test_jcvi: | |
| name: Run jcvi test | |
| needs: append_path | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: nf-test test tests/modules/jcvi.nf.test | |
| clean_finish: | |
| name: Clean workspace after finish | |
| needs: [test_download, test_gffread, test_jcvi] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/[email protected] | |
| - run: rm -rf $GITHUB_WORKSPACE/* |