include nextflow strict parser export #6
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| name: Smoke Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| jobs: | |
| smoke_test: | |
| name: "${{ matrix.profile }} (NF ${{ matrix.nextflow_version }})${{ matrix.quantification_mode && format(' [{0}]', matrix.quantification_mode) || '' }}${{ matrix.bam_only && ' [bam_only]' || '' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| nextflow_version: ["25.04.0", "latest-stable"] | |
| profile: | |
| - test_sc_fastq | |
| - test_sc_bam | |
| - test_sc_multi | |
| - test_visium | |
| - test_custom | |
| include: | |
| - nextflow_version: "latest-stable" | |
| profile: test_sc_fastq | |
| quantification_mode: EM | |
| - nextflow_version: "latest-stable" | |
| profile: test_sc_multi | |
| quantification_mode: EM | |
| - nextflow_version: "latest-stable" | |
| profile: test_sc_fastq | |
| quantification_mode: no_quant | |
| - nextflow_version: "latest-stable" | |
| profile: test_sc_fastq | |
| bam_only: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ matrix.nextflow_version }} | |
| - name: Run ${{ matrix.profile }} | |
| run: | | |
| export NXF_SYNTAX_PARSER=v2 | |
| nextflow run . -profile test_base,${{ matrix.profile }},docker \ | |
| ${{ matrix.quantification_mode && format('--quantification_mode {0}', matrix.quantification_mode) || '' }} \ | |
| ${{ matrix.bam_only && '--bam_only' || '' }} |