include MiXCR toolkit in nf-core/airrflow #298
Workflow file for this run
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| name: Immcantation | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| pull_request: | |
| branches-ignore: | |
| - "master" | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test_container: | |
| name: Run workflow with immcantation devel test_container | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| profile: | |
| [ | |
| "test_assembled_immcantation_devel_hs", | |
| "test_assembled_immcantation_devel_mm", | |
| "test_raw_immcantation_devel", | |
| ] | |
| fail-fast: false | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: logs-${{ matrix.profile }} | |
| path: | | |
| /home/runner/.nextflow.log | |
| /home/runner/work | |
| !/home/runner/work/conda | |
| !/home/runner/work/singularity |