feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines #1089
Workflow file for this run
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| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| name: nf-core CI | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| merge_group: | |
| types: | |
| - checks_requested | |
| branches: | |
| - master | |
| - dev | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFT_VER: "0.9.0" | |
| NFT_WORKDIR: "~" | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}" | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: ["alevin", "cellranger", "cellrangermulti", "kallisto", "star"] | |
| steps: | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Install pdiff to see diff between nf-test snapshots | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pdiff | |
| - uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_VER }} | |
| - name: Run nf-test | |
| run: | | |
| nf-test test \ | |
| --ci \ | |
| --junitxml=test.xml \ | |
| tests/main_pipeline_${{ matrix.profile }}.nf.test | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: test.xml |