v2.2.0 #48
Workflow file for this run
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| name: Automated testing | |
| on: | |
| pull_request: | |
| branches: [ "master" ] | |
| jobs: | |
| container-test-job: | |
| runs-on: ubuntu-20.04 | |
| env: | |
| GM_KEY: ${{ secrets.GM_KEY }} | |
| container: | |
| image: uofgiii/companion:latest | |
| options: --user root | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Run testsuite | |
| run: cd test/testsuite; ./testsuite.rb -threads 2 | |
| - name: Install nextflow | |
| run: | | |
| apt-get -y update; apt-get -y install curl | |
| apt-get -y install openjdk-11-jre-headless; apt-get clean | |
| curl -fsSL get.nextflow.io | bash | |
| - name: Run pipeline | |
| run: NXF_VER=22.10.0 ./nextflow -c loc_github.config -c params_default_kinetoplastid.config run annot.nf -ansi-log false --do_circos=false --run_braker=false |