Visium HD integration #34
Workflow file for this run
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| name: Smoke Tests | |
| on: | |
| pull_request: | |
| branches: [main, devel] | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| smoke_test: | |
| name: "${{ matrix.profile }} (NF ${{ matrix.nextflow_version }})${{ matrix.quantification_mode && format(' [{0}]', matrix.quantification_mode) || '' }}${{ matrix.bam_only && ' [bam_only]' || '' }}${{ matrix.extra_args && format(' [{0}]', matrix.extra_args) || '' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| # Nextflow 26.04.0 - all profiles | |
| - {nextflow_version: "26.04.0", profile: test_sc_fastq} | |
| - {nextflow_version: "26.04.0", profile: test_sc_bam} | |
| - {nextflow_version: "26.04.0", profile: test_sc_multi} | |
| - {nextflow_version: "26.04.0", profile: test_visium} | |
| - {nextflow_version: "26.04.0", profile: test_visium_hd} | |
| - {nextflow_version: "26.04.0", profile: test_custom} | |
| - {nextflow_version: "26.04.0", profile: test_sc_quant_data} | |
| - {nextflow_version: "26.04.0", profile: test_visium_hd_quant_data} | |
| # latest-stable - all profiles (default clusteredEM) | |
| - {nextflow_version: "latest-stable", profile: test_sc_fastq} | |
| - {nextflow_version: "latest-stable", profile: test_sc_bam} | |
| - {nextflow_version: "latest-stable", profile: test_sc_multi} | |
| - {nextflow_version: "latest-stable", profile: test_visium} | |
| - {nextflow_version: "latest-stable", profile: test_visium_hd} | |
| - {nextflow_version: "latest-stable", profile: test_custom} | |
| - {nextflow_version: "latest-stable", profile: test_sc_quant_data} | |
| - {nextflow_version: "latest-stable", profile: test_visium_hd_quant_data} | |
| # latest-stable - extra parameter variants | |
| - {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_visium_hd, quantification_mode: EM} | |
| - {nextflow_version: "latest-stable", profile: test_visium_hd, extra_args: "--banksy false"} | |
| - {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 ${{ matrix.profile }} | |
| run: | | |
| nextflow run . -profile test_base,${{ matrix.profile }},docker \ | |
| ${{ matrix.quantification_mode && format('--quantification_mode {0}', matrix.quantification_mode) || '' }} \ | |
| ${{ matrix.bam_only && '--bam_only' || '' }} \ | |
| ${{ matrix.extra_args || '' }} |