Add merged object information to reference SCE and AnnData files #2050
Workflow file for this run
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| name: Check nextflow stub | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| - development | |
| jobs: | |
| nf-stub-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Setup Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: "21" | |
| distribution: "corretto" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v3 | |
| with: | |
| version: "25.10.4" | |
| - name: Check Nextflow workflow | |
| run: nextflow -log stub-run.log run main.nf -stub -profile stub -ansi-log false | |
| - name: Check Nextflow with checkpoints from previous run | |
| run: nextflow -log checkpoint-run.log run main.nf -stub -profile stub -ansi-log | |
| false | |
| - name: Check Nextflow workflow for building cell type references | |
| run: nextflow -log celltype-ref-run.log run build-celltype-ref.nf -stub -profile | |
| stub -ansi-log false | |
| - name: Check Nextflow workflow for merging objects | |
| run: nextflow -log merge-run.log run merge.nf -stub -profile stub -ansi-log | |
| false --project STUBP01 | |
| - name: Join log files | |
| if: ${{ !cancelled() }} | |
| run: cat stub-run.log checkpoint-run.log celltype-ref-run.log merge-run.log > | |
| nextflow-runs.log | |
| - name: Upload nextflow log | |
| if: ${{ !cancelled() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: nextflow-log | |
| path: nextflow-runs.log |