verified workflows: conditional-gate-on-nonempty-result #3
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Verification workflows | |
| on: | |
| pull_request: | |
| paths: | |
| - "verification/workflows/**" | |
| - "content/verification/**" | |
| - ".github/workflows/verification-workflows.yml" | |
| push: | |
| branches: [main] | |
| paths: | |
| - "verification/workflows/**" | |
| - "content/verification/**" | |
| - ".github/workflows/verification-workflows.yml" | |
| jobs: | |
| planemo: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: false | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| - name: Install Planemo | |
| run: python -m pip install planemo==0.75.41 | |
| - name: Lint verified workflow | |
| continue-on-error: true | |
| shell: bash | |
| run: | | |
| set -euo pipefail | |
| planemo --version | |
| command -v planemo | |
| mapfile -t workflows < <(git ls-files 'verification/workflows/**/*.gxwf.yml') | |
| if [ "${#workflows[@]}" -eq 0 ]; then | |
| echo "No verification workflows found" >&2 | |
| exit 1 | |
| fi | |
| for workflow in "${workflows[@]}"; do | |
| planemo lint "$workflow" | |
| done | |
| - name: Test verified workflow | |
| shell: bash | |
| run: | | |
| set -euo pipefail | |
| mkdir -p upload | |
| mapfile -t workflows < <(git ls-files 'verification/workflows/**/*.gxwf.yml') | |
| if [ "${#workflows[@]}" -eq 0 ]; then | |
| echo "No verification workflows found" >&2 | |
| exit 1 | |
| fi | |
| for workflow in "${workflows[@]}"; do | |
| name="${workflow#verification/workflows/}" | |
| name="${name//\//-}" | |
| name="${name%.gxwf.yml}" | |
| planemo test "$workflow" \ | |
| --galaxy_branch release_25.1 \ | |
| --test_output_json "upload/${name}.json" \ | |
| --test_output "upload/${name}.html" \ | |
| --summary minimal | |
| done | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: verification-workflows-planemo | |
| path: upload/ |