Revert "bigwig writer: parallel indexed read at nproc>1, gated by out… #147
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| name: tests_planemo | |
| on: [push, pull_request, workflow_dispatch] | |
| permissions: | |
| contents: read | |
| env: | |
| GALAXY_BRANCH: release_26.0 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| planemo_test: | |
| name: Planemo test (${{ matrix.tool }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tool: | |
| - alignmentSieve | |
| - bamCompare | |
| - bamCoverage | |
| - bamPEFragmentSize | |
| - bigwigCompare | |
| - bigwigAverage | |
| - computeGCBias | |
| - computeMatrix | |
| - computeMatrixOperations | |
| - correctGCBias | |
| - estimateReadFiltering | |
| - multiBamSummary | |
| - multiBigwigSummary | |
| - plotCorrelation | |
| - plotCoverage | |
| - plotEnrichment | |
| - plotFingerprint | |
| - plotHeatmap | |
| - plotPCA | |
| - plotProfiler | |
| steps: | |
| - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 | |
| with: | |
| persist-credentials: false | |
| - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1 | |
| with: | |
| miniconda-version: "latest" | |
| conda-remove-defaults: true | |
| auto-activate: true | |
| python-version: "3.12" | |
| channels: conda-forge,bioconda | |
| - name: get samtools | |
| run: | | |
| conda install -c conda-forge -c bioconda samtools | |
| - name: pip install | |
| run: | | |
| pip install .[actions] | |
| - name: fix test.bw symlink | |
| run: | | |
| unlink galaxy/wrapper/test-data/test.bw | |
| cp pydeeptools/deeptools/test/test_heatmapper/test.bw galaxy/wrapper/test-data/test.bw | |
| - name: planemo test | |
| run: | | |
| planemo test --no_dependency_resolution \ | |
| --galaxy_branch ${{ env.GALAXY_BRANCH }} \ | |
| --install_galaxy \ | |
| galaxy/wrapper/${{ matrix.tool }}.xml | |
| - name: upload test report | |
| if: always() | |
| uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 | |
| with: | |
| name: "Tool test output ${{ matrix.tool }}" | |
| path: tool_test_output* |