Updating workflows/transcriptomics/rnaseq-pe from 0.4 to 0.5 #924
Workflow file for this run
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| # workflow level env vars cannot be used at the job level | |
| # https://github.community/t/how-to-set-and-access-a-workflow-variable/17335/15 | |
| name: Galaxy Workflow Tests for push and PR | |
| on: [push, pull_request] | |
| env: | |
| GITHUB_USER: iwc-workflows-bot | |
| jobs: | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| uses: ./.github/workflows/setup.yml | |
| with: | |
| python-version-list: "[\"3.7\"]" | |
| galaxy-fork: galaxyproject | |
| galaxy-branch: release_23.1 | |
| max-chunks: 4 | |
| # Planemo lint the changed repositories | |
| lint: | |
| name: Lint workflows | |
| needs: setup | |
| if: needs.setup.outputs.repository-list != '' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - 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_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install wheel | |
| run: pip install wheel | |
| - name: Planemo lint workflows | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: lint | |
| workflows: true | |
| repository-list: "${{ needs.setup.outputs.repository-list }}" | |
| test: | |
| name: Test workflows | |
| needs: setup | |
| if: needs.setup.outputs.repository-list != '' | |
| uses: ./.github/workflows/test_workflows.yml | |
| with: | |
| galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }} | |
| chunk-count: ${{ fromJSON(needs.setup.outputs.chunk-count) }} | |
| chunk-list: ${{ needs.setup.outputs.chunk-list }} | |
| python-version-list: "[\"3.7\"]" | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| galaxy-fork: galaxyproject | |
| galaxy-branch: release_23.1 | |
| check-outputs: false | |
| combine_outputs: | |
| # same as tool step | |
| name: Combine chunked test results | |
| needs: [setup, test] | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| runs-on: ubuntu-latest | |
| 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_{{ needs.setup.outputs.galaxy-head-sha }} | |
| - 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 | |
| # deploy workflows to organization | |
| deploy: | |
| name: Deploy | |
| needs: [setup,test,combine_outputs] | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - 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_{{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install requirements for gen_crates.py | |
| run: pip install -r workflows/requirements.txt | |
| - name: Generate RO-Crate metadata for workflow repositories | |
| run: python workflows/gen_crates.py workflows | |
| - name: Set git user | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "$GITHUB_USER" | |
| git config --global init.defaultBranch main | |
| - uses: fusion-engineering/setup-git-credentials@v2 | |
| with: | |
| credentials: 'https://${{ env.GITHUB_USER }}:${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}@github.com/' | |
| - name: Update or create repositories in github namespace | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: deploy | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| workflows: true | |
| workflow-namespace: iwc-workflows | |
| github-token: ${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }} |