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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| ".": | ||
| - ./.github/workflows/** | ||
| - ./nf-test.config | ||
| - ./nextflow.config | ||
| tests: | ||
| - ./assets/* | ||
| - ./bin/* | ||
| - ./conf/* | ||
| - ./main.nf | ||
| - ./nextflow_schema.json |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,123 +1,68 @@ | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| 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" | ||
| - dev | ||
| pull_request: | ||
| branches: | ||
| - "dev" | ||
| - "master" | ||
| release: | ||
| types: | ||
| - "published" | ||
| types: [published] | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.2" | ||
| NFT_VER: "0.9.0" | ||
| NFT_WORKDIR: "~" | ||
| NFT_DIFF: "pdiff" | ||
| NFT_DIFF_ARGS: "--line-numbers --expand-tabs=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: ${{ steps.list.outputs.tests }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
|
|
||
| - name: Install nf-test | ||
| if: steps.cache-software.outputs.cache-hit != 'true' | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: List nf-test | ||
| id: list | ||
| run: | | ||
| echo "tests=$(nf-test list --silent --format=json tests/pipeline/**/*.nf.test)" >> "$GITHUB_OUTPUT" | ||
| test: | ||
| name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: needs.list.outputs.tests != '[]' | ||
| needs: [list] | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| profile: ["docker"] # TODO , "singularity", "conda"] | ||
| test: ["${{ fromJson(needs.list.outputs.tests) }}"] | ||
| shard: [1, 2, 3, 4] | ||
| NXF_VER: ["latest-stable"] # TODO Test minimum version on release | ||
| profile: ["docker"] | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
|
|
||
| - name: Cache Nextflow installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }} | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
|
|
||
| - name: Run pipeline with test data | ||
| if: steps.cache-software.outputs.cache-hit != 'true' | ||
| - name: Install pdiff to see diff between nf-test snapshots | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash | ||
| sudo mv nf-test /usr/local/bin/ | ||
| python -m pip install --upgrade pip | ||
| pip install pdiff | ||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| - uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Set up miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| - uses: nf-core/setup-nf-test@v1 | ||
| 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 | ||
| version: ${{ env.NFT_VER }} | ||
|
|
||
| - name: Run nf-test | ||
| - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) | ||
| run: | | ||
| nf-test test \ | ||
| --profile="test,${{ matrix.profile }}" \ | ||
| ${{ matrix.test }} \ | ||
| --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml | ||
| --ci \ | ||
| --shard ${{ matrix.shard }}/${{ strategy.job-total }} \ | ||
| --changed-until feat/workflow-updates \ | ||
| --profile "+${{ matrix.profile }}" \ | ||
| --filter pipeline | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: success() || failure() # run this step even if previous step failed | ||
| if: always() # always run even if the previous step fails | ||
| 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 | ||
| report_paths: test.xml |
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