58 add example of non bacterial dataset analysis paper review #7
Workflow file for this run
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| name: Testing long-reads / singularity (ONT) from PR | |
| on: | |
| pull_request: | |
| branches: [ master, dev ] | |
| types: [ opened, synchronize, reopened ] | |
| jobs: | |
| run_nextflow: | |
| name: Run pipeline for the upcoming PR | |
| runs-on: macos-latest | |
| steps: | |
| - name: 'Set up latest Oracle JDK 17' | |
| uses: oracle-actions/setup-java@v1 | |
| with: | |
| website: oracle.com | |
| release: 17 | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - 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: Run tests for long-reads (ont) | |
| run: | | |
| nextflow run main.nf -profile singularity,test,lreads,ont | |
| rm -r work .nextflow* | |
| - name: View results | |
| run: | | |
| sudo apt-get install -y tree | |
| tree lreads_test_ont |