Alignment free deduplication #620
Workflow file for this run
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| VARIANT_CALLER: | |
| - "bcftools" | |
| - "ivar" | |
| CONSENSUS_CALLER: | |
| - "bcftools" | |
| - "ivar" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with small test data with variant caller ${{ matrix.VARIANT_CALLER }} and consensus caller ${{ matrix.CONSENSUS_CALLER }} | |
| env: | |
| VARIANT_CALLER: ${{ matrix.VARIANT_CALLER }} | |
| CONSENSUS_CALLER: ${{ matrix.CONSENSUS_CALLER }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --variant_caller ${VARIANT_CALLER} --consensus_caller ${CONSENSUS_CALLER} --outdir ./results --max_cpus 2 --max_memory 4GB | |
| test-full: | |
| name: Run complete pipeline with more test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run complete pipeline with more test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_full,docker --outdir ./results --max_cpus 4 --max_memory 15GB | |
| test-umi: | |
| name: Run pipeline with test umi data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with umi test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_umi,docker --outdir ./results --max_cpus 2 --max_memory 4GB | |
| test-nothing: | |
| name: Run pipeline and skip everything | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline but skip all steps | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --outdir ./results --max_cpus 2 --max_memory 4GB | |
| test-fail-mapped: | |
| name: Run pipeline with test bad mapping constrained reference | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with umi test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_fail_mapped,docker --outdir ./results --max_cpus 2 --max_memory 4GB | |
| test-fail-db: | |
| name: Run pipeline with test bad database for identifying potential references | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with test data of a bad reference database | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_fail_db,docker --outdir ./results --max_cpus 2 --max_memory 4GB | |
| test-cluster-methods: | |
| name: Run pipeline with minimal test data and different cluster methods | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "latest-everything" | |
| CLUSTER_METHOD: | |
| - "vsearch" | |
| - "mmseqs-cluster" | |
| - "mmseqs-linclust" | |
| - "mash" | |
| - "vrhyme" | |
| - "cdhitest" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with test data and cluster using ${{ matrix.CLUSTER_METHOD }} | |
| env: | |
| CLUSTER_METHOD: ${{ matrix.CLUSTER_METHOD }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --cluster_method ${CLUSTER_METHOD} --skip_iterative_refinement --skip_variant_calling --outdir ./results --max_cpus 4 --max_memory 15GB |