Fix coordinate conversion for BEDPE files #218
Workflow file for this run
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| name: unit tests and docs | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Scala | |
| uses: olafurpg/setup-scala@v12 | |
| with: | |
| java-version: adopt-openj9@1.8.0-292 | |
| - name: Unit Tests | |
| run: | | |
| set -e | |
| ./mill _.test | |
| docs: | |
| name: update tool and metric markdown docs | |
| needs: test | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'pull_request' | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| # To work with the `pull_request` or any other non-`push` even with git-auto-commit | |
| ref: ${{ github.head_ref }} | |
| - name: Setup sdkman | |
| shell: bash -l {0} | |
| run: | | |
| curl -s "https://get.sdkman.io" | bash | |
| source "$HOME/.sdkman/bin/sdkman-init.sh" | |
| sdk version | |
| echo 'source "$HOME/.sdkman/bin/sdkman-init.sh"' >> "$HOME/.bash_profile" | |
| - name: Install tools | |
| shell: bash -l {0} | |
| run: | | |
| sdk install java 8.312.07.1-amzn | |
| sdk install scala 2.13.0 | |
| - name: Build assembly JAR | |
| shell: bash -l {0} | |
| run: | | |
| set -e | |
| ./mill _.deployLocal | |
| - name: Build tool docs | |
| shell: bash -l {0} | |
| run: | | |
| set -e | |
| bash src/scripts/build_tool_docs.sh | |
| - name: Build metric docs | |
| shell: bash -l {0} | |
| run: | | |
| set -e | |
| bash src/scripts/build_metric_docs.sh | |
| - name: Commit generated docs | |
| shell: bash -l {0} | |
| run: | | |
| git add docs/tools/*md | |
| git add docs/*md | |
| git config --global user.name "Github Actions" | |
| git config --global user.email "nobody@fulcrumgenomics.com" | |
| git commit --all --message "Generate docs files" --author "Nobody <nobody@fulcrumgenomics.com>" || echo "nothing to commit" | |
| git push --set-upstream origin "HEAD:${{ github.head_ref }}" --follow-tags --atomic |