Add the option to keep the tags in the new BAM #1
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| name: Planemo | |
| on: [push, pull_request] | |
| env: | |
| GALAXY_BRANCH: release_23.1 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| # setup micromamba doesn't work as galaxy setup by planemo requires conda. | |
| # installing conda over into micromamba built env screws up the PATH | |
| # setup-miniconda + changing over to libmamba to solve is the easiest workaround | |
| jobs: | |
| planemo_test: | |
| name: Planemo test | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| chunk: [1, 2, 3] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-activate-base: true | |
| - name: setup env | |
| run: | | |
| conda env list | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| conda env create -f .github/test_and_build.yml -n test_and_build | |
| - name: pip install | |
| run: | | |
| conda activate test_and_build | |
| pip install . | |
| - name: planemo | |
| run: | | |
| conda activate test_and_build | |
| ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }} | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'Tool test output ${{ matrix.chunk }}' | |
| path: upload | |
| planemo_combine_outputs: | |
| name: Combine chunked test results | |
| needs: planemo_test | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.11'] | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }} | |
| - name: Combine outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: combine | |
| with: | |
| mode: combine | |
| html-report: true | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check |