Run Pipeline Tests #29
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| name: Run Pipeline Tests | |
| on: | |
| workflow_dispatch | |
| env: | |
| NEXTFLOW_VERSION: 23.10.1 | |
| NF_TEST_VERSION: 0.8.3 | |
| AWS_CLI_VERSION: 2.15.19 | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_PUBLIC_KEY }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_KEY }} | |
| AWS_DEFAULT_REGION: 'us-east-1' | |
| 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: Install aws cli | |
| run: curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-${AWS_CLI_VERSION}.zip" -o "awscliv2.zip"; unzip awscliv2.zip; sudo ./aws/install --update | |
| - 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 longest test | |
| run: nf-test test tests/modules/longest.nf.test | |
| - name: Run jcvi test | |
| run: nf-test test tests/modules/jcvi.nf.test | |
| - name: Download synteny module test cds files | |
| run: aws s3 cp s3://synteny-test-data/data/synteny_input/Drosophila_santomea.cds data/synteny_input/Drosophila_santomea.cds; aws s3 cp s3://synteny-test-data/data/synteny_input/Drosophila_simulans.cds data/synteny_input/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 summarise test | |
| run: nf-test test tests/modules/go_summarise.nf.test | |
| - name: Clean workspace after finish | |
| run: rm -rf $GITHUB_WORKSPACE/* |