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Merge pull request #35 from nf-core/nf-core-template-merge-3.0.2
Important! Template update for nf-core/tools v3.0.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,35 @@ | ||
| name: nf-core AWS full size tests | ||
| # This workflow is triggered on published releases. | ||
| # This workflow is triggered on PRs opened against the master branch. | ||
| # It can be additionally triggered manually with GitHub actions workflow dispatch button. | ||
| # It runs the -profile 'test_full' on AWS batch | ||
|
|
||
| on: | ||
| release: | ||
| types: [published] | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| workflow_dispatch: | ||
| pull_request_review: | ||
| types: [submitted] | ||
|
|
||
| jobs: | ||
| run-platform: | ||
| name: Run AWS full tests | ||
| if: github.repository == 'nf-core/createpanelrefs' | ||
| # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered | ||
| if: github.repository == 'nf-core/createpanelrefs' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: octokit/[email protected] | ||
| id: check_approvals | ||
| with: | ||
| route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| - id: test_variables | ||
| if: github.event_name != 'workflow_dispatch' | ||
| run: | | ||
| JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' | ||
| CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') | ||
| test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required | ||
| - name: Launch workflow via Seqera Platform | ||
| uses: seqeralabs/action-tower-launch@v2 | ||
| # TODO nf-core: You can customise AWS full pipeline tests as required | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,200 +1,127 @@ | ||
| # 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 | ||
| pull_request: | ||
| branches: | ||
| - dev | ||
| - master | ||
| release: | ||
| types: | ||
| - "published" | ||
| types: [published] | ||
| workflow_dispatch: | ||
|
|
||
| env: | ||
| NFT_DIFF: "pdiff" | ||
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | ||
| NFT_VER: "0.9.0" | ||
| NFT_WORKDIR: "~" | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.4" | ||
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | ||
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | ||
|
|
||
| # Cancel if a newer run is started | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| 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: | ||
| # Expose matched filters as job 'tags' output variable | ||
| tags: ${{ steps.filter.outputs.changes }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: dorny/paths-filter@v2 | ||
| id: filter | ||
| with: | ||
| filters: "tests/config/tags.yml" | ||
|
|
||
| define_nxf_versions: | ||
| name: Choose nextflow versions to test against depending on target branch | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.nxf_versions.outputs.matrix }} | ||
| steps: | ||
| - id: nxf_versions | ||
| run: | | ||
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | ||
| echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT | ||
| else | ||
| echo matrix='["latest-everything", "23.10.0"]' | tee -a $GITHUB_OUTPUT | ||
| fi | ||
| test-dev: | ||
| if: (github.base_ref == 'dev' || (github.event_name == 'push')) | ||
| name: ${{ matrix.tags }} ${{ matrix.profile }} NXF ${{ matrix.NXF_VER }} | ||
| test: | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/createpanelrefs') }}" | ||
| runs-on: ubuntu-latest | ||
| needs: changes | ||
| name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5" | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| # Run tests based on changes in code | ||
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | ||
| # Only run docker tests on dev branch | ||
| profile: ["docker"] | ||
| # Only test minimal version | ||
| NXF_VER: ["23.10.0"] | ||
| # Always run default test | ||
| include: | ||
| - tags: default | ||
|
|
||
| NXF_VER: | ||
| - "24.04.2" | ||
| - "latest-everything" | ||
| filter: ["workflow", "function", "pipeline"] | ||
| # filter: ["process", "workflow", "function", "pipeline"] | ||
| profile: ["conda", "docker", "singularity"] | ||
| shard: [1, 2, 3, 4] | ||
| # Exclude conda and singularity on dev | ||
| isMaster: | ||
| - ${{ github.base_ref == 'master' }} | ||
| exclude: | ||
| - isMaster: false | ||
| profile: "conda" | ||
| - isMaster: false | ||
| profile: "singularity" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
|
|
||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| fetch-depth: 0 | ||
|
|
||
| - name: Install nf-test | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: Install Nextflow ${{ matrix.NXF_VER }} | ||
| uses: nf-core/[email protected] | ||
| - name: Set up Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
|
|
||
| - name: Run nf-test | ||
| uses: Wandalen/[email protected] | ||
| - name: Set up nf-test | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| command: nf-test test tests/pipeline/${{ matrix.tags }}.nf.test --profile "test,${{ matrix.profile }}" --tap=test.tap | ||
| attempt_limit: 3 | ||
|
|
||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | ||
| version: ${{ env.NFT_VER }} | ||
|
|
||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v2 | ||
| - name: Cache pdiff | ||
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | ||
| id: cache-pip-pdiff | ||
| with: | ||
| name: logs-${{ matrix.profile }} | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/work | ||
| path: ~/.cache/pip | ||
| key: ${{ runner.os }}-pip-pdiff | ||
|
|
||
| test-master: | ||
| # Only run on master branch or when a PR is opened against master | ||
| if: github.base_ref == 'master' | ||
| name: ${{ matrix.tags }} ${{ matrix.profile }} NXF ${{ matrix.NXF_VER }} | ||
| runs-on: ubuntu-latest | ||
| needs: [changes, define_nxf_versions] | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| # Run tests based on changes in code | ||
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | ||
| # Only run docker tests on dev branch | ||
| profile: ["docker", "singularity", "conda"] | ||
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | ||
| # Always run default test | ||
| include: | ||
| - tags: default | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | ||
|
|
||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| - name: Install nf-test | ||
| - name: Set up pdiff to see diff between nf-test snapshots | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: Install Nextflow ${{ matrix.NXF_VER }} | ||
| uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
| python -m pip install --upgrade pip | ||
| pip install pdiff cryptography | ||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
| - name: Set up Apptainer | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-apptainer@main | ||
|
|
||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
| run: | | ||
| mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
| - name: Set up miniconda | ||
| - name: Set up Miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | ||
| with: | ||
| miniconda-version: "latest" | ||
| auto-update-conda: true | ||
| channels: conda-forge,bioconda,defaults | ||
| python-version: ${{ matrix.python-version }} | ||
| conda-solver: libmamba | ||
| channels: conda-forge,bioconda | ||
|
|
||
| - name: Conda clean | ||
| - name: Set up Conda | ||
| if: matrix.profile == 'conda' | ||
| run: conda clean -a | ||
| run: | | ||
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | ||
| echo $(realpath python) >> $GITHUB_PATH | ||
| - name: Run nf-test | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nf-test test tests/pipeline/${{ matrix.tag }}.nf.test --profile "test,${{ matrix.profile }}" --tap=test.tap | ||
| attempt_limit: 3 | ||
| - name: Clean up Disk space | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
|
|
||
| - name: Output log on failure | ||
| if: failure() | ||
| - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/4" | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | ||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v2 | ||
| nf-test test \ | ||
| --ci \ | ||
| --debug \ | ||
| --verbose \ | ||
| --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | ||
| --shard ${{ matrix.shard }}/5 \ | ||
| --changed-since HEAD^ \ | ||
| --follow-dependencies \ | ||
| --profile "+${{ matrix.profile }}" \ | ||
| --filter ${{ matrix.filter }} | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v4 | ||
| if: success() || failure() # always run even if the previous step fails | ||
| with: | ||
| name: logs-${{ matrix.profile }} | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/work | ||
| !/home/runner/pytest_workflow_*/*/work/conda | ||
| !/home/runner/pytest_workflow_*/*/work/singularity | ||
| report_paths: "TEST-*.xml" | ||
|
|
||
| - name: Clean up | ||
| if: always() | ||
| run: | | ||
| sudo rm -rf /home/ubuntu/tests/ |
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