Updating workflows/transcriptomics/rnaseq-sr from 1.1 to 1.2 #2976
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: | |
| paths-ignore: | |
| - '**/*.md' | |
| - 'scripts/**' | |
| - 'website/**' | |
| pull_request: | |
| paths-ignore: | |
| - '**/*.md' | |
| - 'scripts/**' | |
| - 'website/**' | |
| env: | |
| GITHUB_USER: iwc-workflows-bot | |
| jobs: | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| uses: ./.github/workflows/setup.yml | |
| with: | |
| python-version-list: "[\"3.11\"]" | |
| max-chunks: 4 | |
| galaxy-fork: galaxyproject | |
| galaxy-branch: release_24.1 | |
| # 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: ['3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install wheel | |
| run: pip install wheel | |
| - name: Planemo lint workflows | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: lint | |
| with: | |
| mode: lint | |
| workflows: true | |
| repository-list: "${{ needs.setup.outputs.repository-list }}" | |
| additional-planemo-options: --iwc | |
| 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: "[\"3.11\"]" | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| galaxy-fork: galaxyproject | |
| galaxy-branch: release_24.1 | |
| check-outputs: false | |
| combine_outputs: | |
| # same as tool step | |
| name: Combine chunked test results | |
| needs: [setup, test] | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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 | |
| markdown-report: true | |
| - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY | |
| - name: Save PR number | |
| run: echo ${{ github.event.number }} > ./upload/NR | |
| - name: Debug PR number | |
| run: | | |
| cat ./upload/NR | |
| - uses: actions/upload-artifact@v4 | |
| 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: ['3.11'] | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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 }} | |
| deploy-report: | |
| name: Report deploy status | |
| needs: [deploy] | |
| if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| # report to the PR if deployment failed | |
| - name: Get PR object | |
| uses: 8BitJonny/[email protected] | |
| id: getpr | |
| with: | |
| sha: ${{ github.event.after }} | |
| - name: Create comment | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| issue-number: ${{ steps.getpr.outputs.number }} | |
| body: | | |
| Attention: deployment ${{ needs.deploy.result }}! | |
| https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| determine-success: | |
| name: Check workflow success | |
| needs: [setup, lint, combine_outputs] | |
| if: ${{ always() && github.ref != 'refs/heads/main' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check status | |
| if: ${{ needs.combine_outputs.result != 'skipped' && (needs.lint.result != 'success' || needs.combine_outputs.result != 'success') }} | |
| run: exit 1 |