Update rnaseq.wdl #10
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| name: Auto-Build WDL Graphs | |
| on: | |
| push: | |
| paths: | |
| - "workflows/**/*.wdl" | |
| pull_request: | |
| paths: | |
| - "workflows/**/*.wdl" | |
| workflow_dispatch: | |
| jobs: | |
| build-graphs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Set up Java (for womtool) | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: temurin | |
| java-version: 17 | |
| - name: Install Graphviz | |
| run: sudo apt-get update && sudo apt-get install -y graphviz | |
| - name: Download womtool | |
| run: | | |
| mkdir -p tools | |
| curl -L -o tools/womtool.jar https://github.com/broadinstitute/cromwell/releases/download/90/womtool-90.jar | |
| - name: Detect changed WDLs | |
| id: changed | |
| run: | | |
| # Detect added or modified WDLs in workflows/ | |
| files=$(git diff --name-only HEAD~1 HEAD | grep '^workflows/.*\.wdl$' || true) | |
| echo "changed_files=$files" >> $GITHUB_OUTPUT | |
| echo "Changed WDL files:" | |
| echo "$files" | |
| - name: Build graphs for changed WDLs | |
| if: steps.changed.outputs.changed_files != '' | |
| run: | | |
| echo "${{ steps.changed.outputs.changed_files }}" | while read -r wdl; do | |
| [ -z "$wdl" ] && continue | |
| dir=$(dirname "$wdl") | |
| base=$(basename "$wdl" .wdl) | |
| dot="${dir}/${base}.dot" | |
| png="${dir}/${base}.png" | |
| echo "Building graph for $wdl" | |
| java -jar tools/womtool.jar graph "$wdl" > "$dot" | |
| dot -Tpng "$dot" -o "$png" | |
| done | |
| - name: Commit and push graphs | |
| if: steps.changed.outputs.changed_files != '' | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git add workflows/**/*.dot workflows/**/*.png || true | |
| git commit -m "Auto-update WDL workflow graphs" || echo "No changes to commit" | |
| git push |