Wrap up v3.3.3 #8
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| name: Testing new PR with docker | |
| on: | |
| pull_request: | |
| branches: [master, dev] | |
| types: [ opened, synchronize, reopened ] | |
| jobs: | |
| run_nextflow: | |
| name: Run pipeline for the upcoming PR | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Clean environment | |
| run: | | |
| sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android | |
| sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET | |
| - name: Get database | |
| run: | | |
| nextflow run main.nf -profile docker --get_zenodo_db --output ./zenodo_db --max_memory '6.GB' --max_cpus 2 | |
| sudo rm -r work .nextflow* | |
| yes | docker system prune | |
| - name: Run quicktest profile | |
| run: | | |
| nextflow run main.nf -profile docker,quicktest --bacannot_db $( realpath ./zenodo_db/bac* ) --output ./results --max_memory '6.GB' --max_cpus 2 | |
| sudo rm -r work .nextflow* | |
| yes | docker system prune | |
| - name: View results | |
| run: | | |
| sudo apt-get install -y tree | |
| tree ./results |