refactor: expose nf plugin; set version #23
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| name: run_test_pipelines | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker login (if required for pulling private images) | |
| if: env.DOCKER_USERNAME && env.DOCKER_PASSWORD | |
| run: | | |
| echo "${{ secrets.DOCKER_PASSWORD }}" | docker login -u "${{ secrets.DOCKER_USERNAME }}" --password-stdin | |
| - name: Set up Nextflow | |
| run: | | |
| curl -s https://get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run Nextflow Illumina AQUASCOPE with Docker | |
| run: | | |
| nextflow run main.nf --resume -profile docker,test_illumina -entry AQUASCOPE --outdir ~/projects/complete | |
| - name: Set up Singularity | |
| uses: singularityhub/install-singularity@main | |
| - name: Run Nextflow Illumina QUALITY_ALIGN with Singularity | |
| run: nextflow run main.nf --resume -profile singularity,test_illumina -entry QUALITY_ALIGN --outdir ~/projects/illumina/quality | |
| - name: Run Nextflow Illumina AQUASCOPE with Singularity | |
| run: nextflow run main.nf --resume -profile singularity,test_illumina -entry AQUASCOPE --outdir ~/projects/illumina/complete | |
| - name: Run Nextflow Illumina FREYJA with Singularity | |
| run: nextflow run main.nf --resume -profile singularity,test_bam -entry FREYJA_ONLY --outdir ~/projects/bam/complete | |
| - name: Run Nextflow Ion Torrent AQUASCOPE with Singularity | |
| run: nextflow run main.nf --resume -profile singularity,test_iontorrent -entry AQUASCOPE --outdir ~/projects/iontorrent/complete | |
| - name: Run Nextflow ONT AQUASCOPE with Singularity | |
| run: nextflow run main.nf --resume -profile singularity,test_ont -entry AQUASCOPE --outdir ~/projects/ont/complete |