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Merge pull request #71 from Plant-Food-Research-Open/add/nftest
Integrated nf-test into pipeline CI
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| ".": | ||
| - ./.github/workflows/** | ||
| - ./nf-test.config | ||
| tests: | ||
| - ./assets/* | ||
| - ./bin/* | ||
| - ./conf/* | ||
| - ./main.nf | ||
| - ./nextflow_schema.json | ||
| - ./nextflow.config |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -5,45 +5,96 @@ on: | |
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| env: | ||
| NXF_ANSI_LOG: false | ||
| NFT_WORKDIR: "nf-test-work" | ||
| 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: | ||
| nf-test-changes: | ||
| name: Check for changes | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| nf_test_files: ${{ steps.list.outputs.components }} | ||
| steps: | ||
| - uses: actions/[email protected] | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - name: List nf-test files | ||
| id: list | ||
| uses: adamrtalbot/[email protected] | ||
| with: | ||
| head: ${{ github.sha }} | ||
| base: origin/${{ github.base_ref }} | ||
| include: .github/include.yaml | ||
|
|
||
| - name: print list of nf-test files | ||
| run: | | ||
| echo ${{ steps.list.outputs.components }} | ||
| test: | ||
| name: Run pipeline with test data | ||
| name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} | ||
| needs: [nf-test-changes] | ||
| if: needs.nf-test-changes.outputs.nf_test_files != '[]' | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "24.04.2" | ||
| TEST_PARAMS: | ||
| - minimal | ||
| - short | ||
| - nonmasked | ||
| - stub | ||
| OPTION_STUB: | ||
| - "-stub" | ||
|
|
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| nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | ||
| profile: | ||
| - "docker" | ||
|
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||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
| uses: actions/checkout@v4.2.1 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - uses: actions/[email protected] | ||
| with: | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
|
|
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| - name: Install pdiff to see diff between nf-test snapshots | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pdiff | ||
| - uses: nf-core/[email protected] | ||
| with: | ||
| version: 0.9.0 | ||
|
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||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
| if: matrix.nf_test_files == 'tests/stub/main.nf.test' | ||
| uses: jlumbroso/[email protected] | ||
|
|
||
| - name: Run nf-test | ||
| run: | | ||
| nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" | ||
| confirm-pass: | ||
| runs-on: ubuntu-latest | ||
| needs: [test] | ||
| if: always() | ||
| steps: | ||
| - name: All tests ok | ||
| if: ${{ !contains(needs.*.result, 'failure') }} | ||
| run: exit 0 | ||
| - name: One or more tests failed | ||
| if: ${{ contains(needs.*.result, 'failure') }} | ||
| run: exit 1 | ||
|
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||
| - name: Run pipeline with test data | ||
| - name: debug-print | ||
| if: always() | ||
| run: | | ||
| nextflow run \ | ||
| ${GITHUB_WORKSPACE} \ | ||
| -profile test,docker \ | ||
| -params-file \ | ||
| ./tests/${{ matrix.TEST_PARAMS }}/params.json \ | ||
| ${{ matrix.OPTION_STUB }} \ | ||
| --outdir ./results | ||
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,3 +9,7 @@ do | |
| rm -rf "work/$i" | ||
| done | ||
| echo "Cleaned work..." | ||
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| rm -f .nf-test.log | ||
| rm -rf .nf-test | ||
| echo "Cleaned nf-test..." | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - conda-forge::pigz=2.3.4 |
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