Run Pipeline Tests #18
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: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clean workspace before start | |
| run: rm -rf $GITHUB_WORKSPACE/* | |
| - uses: actions/[email protected] | |
| - name: Set up JDK 11 | |
| uses: actions/[email protected] | |
| with: | |
| java-version: '11' | |
| distribution: 'adopt' | |
| - name: Install nextflow | |
| run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow; | |
| - name: Install nf-test | |
| 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" | |
| - name: Add software to path | |
| run: echo "/opt" >> $GITHUB_PATH; | |
| - name: Run ncbi_download test | |
| run: nf-test test tests/modules/download_ncbi.nf.test | |
| - name: Run gffread test | |
| run: nf-test test tests/modules/gffread.nf.test | |
| - name: Run jcvi test | |
| run: nf-test test tests/modules/jcvi.nf.test | |
| - name: download synteny test cds files | |
| run: cd data/synteny_input; wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1-sgGEBdkcDiw2XHwuapH53HCdzeil-F1' -O Drosophila_santomea.cds; wget --no-check-certificate 'https://docs.google.com/uc?export=download&id='1Sc8rD8ioxBJPIxZoCPkY_IkCBX1L_LwL -O Drosophila_simulans.cds | |
| - name: Run synteny test | |
| run: nf-test test tests/modules/synteny.nf.test | |
| - name: Run chromopaint test | |
| run: nf-test test tests/modules/chromo.nf.test | |
| - name: Run score test | |
| run: nf-test test tests/modules/score.nf.test | |
| - name: Run score_tree test | |
| run: nf-test test tests/modules/score_tree.nf.test | |
| - name: Run go test | |
| run: nf-test test tests/modules/go.nf.test | |
| - name: Run go test | |
| run: nf-test test tests/modules/go_summarise.nf.test | |
| - name: Clean workspace after finish | |
| run: rm -rf $GITHUB_WORKSPACE/* |