Now correctly validating gff files for circular sequences #151
Workflow file for this run
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'plant-food-research-open/assemblyqc') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| TEST_PARAMS: | |
| - minimal | |
| - invalid | |
| - stub | |
| - noltr | |
| - hicparam | |
| include: | |
| - OPTION_STUB: "" | |
| - OPTION_STUB: "-stub" | |
| TEST_PARAMS: stub | |
| - OPTION_STUB: "-stub" | |
| TEST_PARAMS: hicparam | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ matrix.NXF_VER }} | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run \ | |
| ${GITHUB_WORKSPACE} \ | |
| --outdir ./results \ | |
| -profile docker \ | |
| -params-file \ | |
| ./tests/${{ matrix.TEST_PARAMS }}/params.json \ | |
| ${{ matrix.OPTION_STUB }} | |
| nf-test: | |
| name: Run nf-tests | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'plant-food-research-open/assemblyqc') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ matrix.NXF_VER }} | |
| - name: Install nf-test | |
| uses: nf-core/[email protected] | |
| - name: Run nf-tests | |
| run: | | |
| nf-test \ | |
| test \ | |
| --verbose \ | |
| tests |