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Merge pull request #18 from CarsonJM/development
Fixed nf-tests, restructured test-data, and started fixing failing tests
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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 |
|---|---|---|
| @@ -1,43 +1,135 @@ | ||
| name: nf-core CI | ||
| # 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: | ||
| release: | ||
| types: [published] | ||
| merge_group: | ||
| types: | ||
| - checks_requested | ||
| branches: | ||
| - master | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFT_VER: "0.8.4" | ||
| 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: | ||
| changes: | ||
| name: Check for changes | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| nf_test_files: ${{ steps.list.outputs.components }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| 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 ${{ steps.list.outputs.components }} | ||
| test: | ||
| name: Run pipeline with test data | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'hofflab/biobakerymgx') }}" | ||
| name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} | ||
| needs: [changes] | ||
| if: needs.changes.outputs.nf_test_files != '[]' | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| - "23.04" | ||
| nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"] | ||
| profile: | ||
| - "docker" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data | ||
| # TODO nf-core: You can customise CI pipeline run tests as required | ||
| # For example: adding multiple test runs with different parameters | ||
| # Remember that you can parallelise this by using strategy.matrix | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
|
|
||
| - name: Install pdiff to see diff between nf-test snapshots | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pdiff | ||
| - name: Cache nf-test installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest | ||
|
|
||
| - 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: Run nf-test | ||
| run: | | ||
| nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap | ||
| - uses: pcolby/tap-summary@v1 | ||
| with: | ||
| path: >- | ||
| test.tap | ||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: always() # always run even if the previous step fails | ||
| with: | ||
| report_paths: test.xml | ||
|
|
||
| confirm-pass: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - changes | ||
| - 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 | ||
|
|
||
| - name: debug-print | ||
| if: always() | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| name: Test successful pipeline download with 'nf-core download' | ||
|
|
||
| # Run the workflow when: | ||
| # - dispatched manually | ||
| # - when a PR is opened or reopened to master branch | ||
| # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| testbranch: | ||
| description: "The specific branch you wish to utilize for the test execution of nf-core download." | ||
| required: true | ||
| default: "dev" | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| branches: | ||
| - master | ||
| pull_request_target: | ||
| branches: | ||
| - master | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| jobs: | ||
| download: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 | ||
|
|
||
| - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | ||
| with: | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
| - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install git+https://github.com/nf-core/tools.git@dev | ||
| - name: Get the repository name and current branch set as environment variable | ||
| run: | | ||
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} | ||
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} | ||
| echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} | ||
| - name: Download the pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| run: | | ||
| nf-core download ${{ env.REPO_LOWERCASE }} \ | ||
| --revision ${{ env.REPO_BRANCH }} \ | ||
| --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ | ||
| --compress "none" \ | ||
| --container-system 'singularity' \ | ||
| --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ | ||
| --container-cache-utilisation 'amend' \ | ||
| --download-configuration | ||
| - name: Inspect download | ||
| run: tree ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Run the downloaded pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results |
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