Update Citations #340
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 assembly test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with assembly test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_assembly_only,docker --outdir ./results | |
| profile: | |
| name: Run additional profile tests | |
| # 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/metapep') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tests: ["test_bins", "test_coassembly", "test_model_information"] # add further test profiles here, will be run in parallel (but only with one nextflow version) | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with profile ${{ matrix.tests }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results | |
| all_profiles: | |
| name: Run all additional profile tests that require ncbi credentials | |
| # Only run on PRs from branches of nf-core/metapep repository or on push if this is the nf-core dev branch (merged PRs) | |
| # (GitHub secrets are not accessible for workflows from forks) | |
| if: ${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tests: ["test", "test_mouse", "test_tiny"] # add further test profiles here, will be run in parallel (but only with one nextflow version) | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with profile ${{ matrix.tests }} | |
| env: | |
| NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }} | |
| NCBI_KEY: ${{ secrets.NCBI_KEY }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --ncbi_email "$NCBI_EMAIL" --ncbi_key "$NCBI_KEY" --outdir ./results |