set specific ubuntu version for CI #62
Workflow file for this run
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
| # This is a basic workflow to help you get started with Actions | |
| name: CI | |
| # Controls when the action will run. | |
| # Triggers the workflow on push or pull request events | |
| on: [push, pull_request, workflow_dispatch] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a second job called "build2" | |
| test_aline: | |
| # avoid to run twice push and PR | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu:24.04 | |
| services: | |
| docker: | |
| image: docker:dind | |
| options: --privileged --shm-size=2g | |
| volumes: | |
| - /var/run/docker.sock:/var/run/docker.sock:ro | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Install/cache OpenJDK | |
| - name: Cache OpenJDK | |
| id: cache-openjdk | |
| uses: actions/cache@v3 | |
| with: | |
| path: /usr/lib/jvm/java-11-openjdk-amd64 | |
| key: ${{ runner.os }}-openjdk-11 | |
| restore-keys: | | |
| ${{ runner.os }}-openjdk-11 | |
| - name: Install openjdk | |
| if: ${{ steps.cache-openjdk.outputs.cache-hit != 'true' }} | |
| run: sudo apt-get install openjdk-11-jdk | |
| # Install/cache nextflow | |
| - name: Cache nextflow | |
| id: cache-nextflow | |
| uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }}-nextflow | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow | |
| - name: Install Nextflox | |
| if: ${{ steps.cache-nextflow.outputs.cache-hit != 'true' }} | |
| run: curl -s https://get.nextflow.io | bash && mv nextflow /usr/local/bin && chmod +x /usr/local/bin/nextflow | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| # Run tests sequentialy | |
| - name: test short single | |
| run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf | |
| - name: test short paired | |
| run: nextflow run -ansi-log -profile docker,test_illumina_paired aline.nf | |
| - name: test ont | |
| run: nextflow run -ansi-log -profile docker,test_ont aline.nf | |
| - name: test pacbio | |
| run: nextflow run -ansi-log -profile docker,test_pacbio aline.nf |