Run Pipeline Tests #1
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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/local/download_ncbi.nf.test | |
| - name: Run gffread test | |
| run: nf-test test tests/modules/local/gffread.nf.test | |
| - name: Run get data test | |
| run: nf-test test tests/modules/local/getdata.nf.test | |
| - name: Run orthofinder test | |
| run: nf-test test tests/modules/local/orthofinder.nf.test | |
| - name: Run cafe test | |
| run: nf-test test tests/modules/local/cafe.nf.test | |
| - name: Run cafe_go test | |
| run: nf-test test tests/modules/local/cafe_go.nf.test | |
| #- name: Run chromo_go test (Not needed as this module is not in final pipeline [for now]) | |
| # run: nf-test test tests/modules/local/chromo_go.nf.test | |
| - name: Run go assign test | |
| run: nf-test test tests/modules/local/go_assign.nf.test | |
| #- name: Run go expansion test (Not needed as this module is not in final pipeline [for now]) | |
| # run: nf-test test tests/modules/local/go_expansion.nf.test | |
| - name: Download aws module test cds files | |
| run: aws s3 cp s3://excon/data/Insect_data/fasta/* data/; aws s3 cp s3://excon/data/Insect_data/gofiles/* data/ | |
| - name: Clean workspace after finish | |
| run: rm -rf $GITHUB_WORKSPACE/* |