Use install-gh-release GitHub Action #811
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: | ||
| branches: | ||
| - "dev" | ||
| - "master" | ||
| release: | ||
| types: | ||
| - "published" | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.2" | ||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
| jobs: | ||
| list: | ||
| name: List Tests | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | ||
| outputs: | ||
| # Expose matched filters as job 'modules' output variable | ||
| tests: ${{ steps.list.outputs.tests }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Setup Nextflow | ||
| uses: jaxxstorm/[email protected] | ||
| with: | ||
| repo: nextflow-io/nextflow | ||
| tag: v23.10.0 | ||
| cache: enable | ||
| - name: Setup nf-test | ||
| uses: jaxxstorm/[email protected] | ||
| with: | ||
| repo: https://github.com/askimed/nf-test | ||
| tag: "${{ NFTEST_VER }}" | ||
|
Check failure on line 45 in .github/workflows/ci.yml
|
||
| cache: enable | ||
| - name: List nf-test | ||
| id: list | ||
| run: | | ||
| echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT" | ||
| test: | ||
| name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: needs.list.outputs.tests != '[]' | ||
| needs: [list] | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| profile: ["docker"] # TODO , "singularity", "conda"] | ||
| test: ["${{ fromJson(needs.list.outputs.tests) }}"] | ||
| exclude: | ||
| - test: "tests/subworkflows/local/grohmm/main.nf.test@3508b8c9" | ||
| - test: "tests/subworkflows/local/grohmm/main.nf.test@716555be" | ||
| - test: "tests/subworkflows/local/grohmm/main.nf.test@306b4b15" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
| - name: Setup Nextflow | ||
| uses: jaxxstorm/[email protected] | ||
| with: | ||
| repo: nextflow-io/nextflow | ||
| tag: v23.10.0 | ||
| cache: enable | ||
| - name: Setup nf-test | ||
| uses: jaxxstorm/[email protected] | ||
| with: | ||
| repo: https://github.com/askimed/nf-test | ||
| tag: "${{ NFTEST_VER }}" | ||
| cache: enable | ||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
| - name: Set up miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| channels: conda-forge,bioconda,defaults | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Conda clean | ||
| if: matrix.profile == 'conda' | ||
| run: conda clean -a | ||
| - name: Run nf-test | ||
| run: | | ||
| nf-test test \ | ||
| --profile="test,${{ matrix.profile }}" \ | ||
| ${{ matrix.test }} \ | ||
| --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: success() || failure() # run this step even if previous step failed | ||
| with: | ||
| path: ${{ matrix.test }}-${{ matrix.profile }}.xml | ||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml | ||
