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Merge pull request #1096 from nf-core/dev
Release candidate 3.2.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| name: pytest-workflow-release | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| on: | ||
| pull_request: | ||
| branches: [master] | ||
| release: | ||
| types: [published] | ||
|
|
||
| # Cancel if a newer run is started | ||
| 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: | ||
| # 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" | ||
|
|
||
| test: | ||
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | ||
| runs-on: ubuntu-latest | ||
| needs: changes | ||
| if: needs.changes.outputs.tags != '[]' | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | ||
| profile: ["docker", "singularity"] | ||
| TEST_DATA_BASE: | ||
| - "test-datasets/data" | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| exclude: | ||
| - profile: "singularity" | ||
| tags: concatenate_vcfs | ||
| - profile: "singularity" | ||
| tags: merge | ||
| - profile: "singularity" | ||
| tags: validation_checks | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Hash Github Workspace | ||
| id: hash_workspace | ||
| run: | | ||
| echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | ||
| - name: Cache test data | ||
| id: cache-testdata | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: test-datasets/ | ||
| key: ${{ steps.hash_workspace.outputs.digest }} | ||
|
|
||
| - name: Check out test data | ||
| if: steps.cache-testdata.outputs.cache-hit != 'true' | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: nf-core/test-datasets | ||
| ref: sarek3 | ||
| path: test-datasets/ | ||
|
|
||
| - name: Replace remote paths in samplesheets | ||
| run: | | ||
| for f in tests/csv/3.0/*csv; do | ||
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f | ||
| echo "========== $f ============" | ||
| cat $f | ||
| echo "========================================" | ||
| done; | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: "3.x" | ||
|
|
||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: ~/.cache/pip | ||
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-pip- | ||
| - name: Install Python dependencies | ||
| run: python -m pip install --upgrade pip pytest-workflow | ||
|
|
||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| - name: Install Nextflow ${{ matrix.NXF_VER }} | ||
| uses: nf-core/setup-nextflow@v1.2.0 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - 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: ${{ matrix.python-version }} | ||
|
|
||
| - name: Conda clean | ||
| if: matrix.profile == 'conda' | ||
| run: conda clean -a | ||
|
|
||
| - name: Run pytest-workflow | ||
| uses: Wandalen/wretry.action@v1.0.11 | ||
| with: | ||
| command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | ||
| attempt_limit: 3 | ||
|
|
||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | ||
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: logs-${{ 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 |
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